by de Buhr, Svenja and Gräter, Frauke

This dataset on Abl kinase's allosteric regulation was created using Molecular Dynamics Simulations using Gromacs and Plumed, and analyzed using Gromacs tools, Plumed, FDA and ConAn. c-Abl kinase, a key signalling hub in many biological processes ranging from cell development to proliferation, is tightly regulated by two inhibitory Src homology domains. An N-terminal myristoyl-modification (Myr) can bind to a hydrophobic pocket in the kinase C-lobe, which stabilizes the auto-inhibitory assembly. Activation is triggered by Myr release. We used molecular dynamics simulations to show how both Myr and the Src homology (SH) domains are required to impose the full inhibitory effect on the kinase domain, and reveal the allosteric transmission pathway at residue-level resolution. In detail, we created Abl models with different conformations of the kinase C-terminal helix (alpha_I helix) critical for Myr binding and compared their equilibrium dynamics in the presence or absence of the SH domains or Myr. We deciphered allosteric pathways between the Myr binding site and the kinase active site by analyzing forces between protein residues. We futher investigated how the critical alpha_I helix changes its conformation using Metadynamics simulations and used output structures of these simulations for Free Energy calculation of Myr unbinding by means of Umbrella Sampling. Importantly, we find Myr insertion into a membrane to thermodynamically compete with binding to the Abl kinase domain. Myr thus not only localizes the protein to the cellular membrane, but membrane attachment at the same time enhances activation of c-Abl by stabilizing its pre-activated state. Our data put forward a model in which lipidation tightly couples kinase localization and regulation, a scheme that currently appears to be unique for this non-receptor tyrosine kinase.

Description of the data and file structure

The files include simulation input files (.mdp, .itp, .top, .gro, .tpr), as well as post-processing files (.xvg, .dat). Thorough documentation of the file formats can be accessed here: https://manual.gromacs.org/documentation/2020/reference-manual/file-formats.html. The steps that were conducted to run the simulations are provided in text format or as executable bash scripts.

There is a folder for each Abl model (kinase only and SH3-SH2-kinase models) that was simulated under equilibrium conditions, one folder containing the exact force field version used throughout the study and a folder for each larger analysis: force distribution analysis (FDA), Metadynamics, principal component analysis (PCA) and Umbrella sampling. The directory tree is provided at the bottom of this README.

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Folders named after protein models

There is a folder containing the simulation and analysis files for each Abl model:

• SH3-SH2-KD_Myr, SH3-SH2-KD_noMyr, kinase_kinked_Myr, kinase_kinked_noMyr, kinase_straight_Myr, kinase_straight_noMyr, kinase_active:
  • kinase-only models with a straight or kinked alpha_I helix
  • kinase-only model in an active conformation
  • SH3-SH2-kinase model
  • Each model was simulated with and without myristoyl (Myr). These folders contain the simulation files to be used with the Gromacs software for two sets of simulations that differ in the choice of thermostat.
• simulation parameters (.mdp)
  • for the equilibration (nvt and npt ensemble) and production simulation
  • for details on the parameters refer to https://manual.gromacs.org/2020/user-guide/mdp-options.html
• starting structures (.gro) detailing the atomic positions
  • the modelled protein with ATP, MG and Myr (system.gro),
  • inserted in the simulation box (system_box.gro),
  • after solvent addition (system_solv.gro),
  • after ionization/neutralization (system_solv_ions.gro) and
  • after energy minimization (system_em.gro)
• topologies (.top, .itp) listing atom and corresponding connectivity parameters
  • master topology (topol.top)
  • include files (protein.itp, ATP.itp, MD.itp, MYR.itp) and position restraints (posre_* .itp)
• index file (index.ndx) listing atom indices that belong to a certain group such as the protein, membrane, solvent, ions, etc.

A subfolder for each replicate contains simulation start files an raw data files obtained through analysis with Gromacs tools and Plumed. The replicate numbers range from 11-20 and 21-30 for simulation set1 and set2, respectively. The simulation sets differ in the choice of temperature control method as detailed in the Methods section of the accompanying publication.

• .tpr files contain all information needed for a single simulation and can be used to rerun each simulation.
• helicity.dat: measure of helicity of Abl's alpha_I helix over time obtained using the Plumed alpharmsd collective variable
• rmsd_noIa_bb.xvg: RMSD of Abl's kinase domain backbone atoms excluding the alpha_I helix over time
• rmsf.xvg: RMSF for each residue of Abl's kinase domain

The ConAn subfolder within the SH3-SH2-KD_noMyr folder contains files obtained through the ConAn software, which was used to analyze the contacts between Abl's kinase domain and SH2 domain.

• subfolder for each replicate including
  • contact matrices for timepoints analyzed every 200 ps (.dat files)
  • KD-SH2_dist.xvg: distance between the kinase domain and SH2 domain over time
• SH2-KD_av_contacts_reps.csv: average number of contacts for each replicate (rep) between the SH2 domain and the kinase domain excluding the alpha_I helix (core) and between the SH2 domain and the alpha_I helix (Ialpha)
• SH2-KD_contacts_native.csv: number of contacts (count) between each residue pair (pair), indicated by residue indices
• SH2-KD_median_contacts_time.csv: median number of contacts between kinase and SH2 domain over time

FDA

This folder contains the files needed for and obtained through the FDA analysis program. Refer to the FDA documentation for further details about the file types https://github.com/HITS-MBM/gromacs-fda.

• diff* .pdb: files obtained using the fda_graph tool, used to visualize force differences between indicated Abl models. Force differences are written as bonds exploiting the CONECT feature of pdb files. The files are named the following way: diff_{comparison}_{property}_graph_{network}-{cutoff}.pdb
  • comparison: force differences are calculated between two models, i.e. between kinase-only and SH3-SH2-kinase (KD-whole), between a kinase with a kinked and staight alpha_I helix (kinked-straight), or between a kinase with or without Myr (Myr-noMyr)
  • property: additional property of the compared models, i.e. do they contain Myr or not, is the alpha_I helix in the kinked or straight conformation
  • network: minimum size of a connected force difference cluster. If 'big' is written, only the biggest force difference cluster is written to the file
  • cutoff: force cutoff for the force differences between the models
• diff_{comparison}_{property}.pfr: raw force differences between models. These files are obtained by subtracting forces written into the .pfr files of individual models using the the FDA.ipynb script (explained below). Files are named equivalently to the diff* .pdb files explained above. Contents are visualized with the help of the diff* .pdb files.
• FDA.ipynb: jupyter notebook python script. Reads .pfr files and calculates the differences between two models
• input.pfi: input parameters for FDA analysis
• .tga: image of force differences (diff* .pdb) visualized and rendered using vmd
• .gro, .ndx, .tpr, .xtc are files needed as input for FDA analysis
  • .xtc files are Gromacs trajectories containing only the protein atoms. They are written every 200 ps, excluding the first 1000 ns of the simulations. The files are named after each Abl model and replicate number. Files with 'concat' in their name contain the concatenated trajectories for each model.
  • .gro: Atomic structure file for each model including the protein atoms only, needed for force difference visualization
  • .ndx: Index files matching the protein only .gro file
  • .tpr: Run input file for the protein atoms only.
• .edr, .log, .trr: Outputs of the FDA rerun containing the energies, logs and trajectories including atom forces and velocities, respectively
• .pfr: Output obtained during FDA analysis. Contains forces between residue pairs
• start_fda.sh: Bash script that submits an FDA run for each model
• steps: commented list of commands performed during FDA analysis
• submit.sh: Used by start_fda.sh script to submit the FDA run to a compute cluster. It includes the software version and exact command given to Gromacs FDA.
• vis_diff* _Fig1.tcl: scripts to be used with the molecular visualization program vmd. Reads the diff* .pfr files and matching .gro files to display force differences

ff

This folder contains the force field used for all simulations: The Charmm36m force field, March 2019 version, for use with the Gromacs simulation software. Downloaded from the Mackarell Lab website: http://mackerell.umaryland.edu/charmm_ff.shtml

Metadynamics

This folder contains the input files and results of the Metadynamics simulations (metad) as well as simulation files of the equilibrium simulations performed using Metadynamics frames as start structures (eq_after_metad).
The metad folder contains a protein reference structure and subfolders for each tested Metadynamics condition. Folders named s* indicate the width/sigma of the added gaussians: s2 and s3 stand for a sigma of 0.02 and 0.03 nm, respectively. Subfolders therein mark the applied bias factor (bf*) and, if applicable, the number of replicate simulations.

• COLVAR: Plumed output containing the value of the alpharmsd collective variable over time during the Metadynamics simulations
• HILLS: Plumed output containing the height of the gaussians deposited during the Metadynamics simulations
• KD-SH2_dist.xvg: Distance between the kinase domain and SH2 domain over time
• md.tpr: Simulation input file
• plumed.dat: File providing the input parameters for the Plumed software.

The eq_after_metad folder includes results from simulations that were started from frames extracted form Metadynamics simulations. There is one folder for each replicate simulation named the following way:
s{sigma value}_bf{bias factor}_r{replicate}-fr{frame}ns

• sigma value,bias factor: gaussian width and bias factor that was used for the Metadynamics simulation from the the start frame for the simulation was taken
• replicate: replicate number of the Metadynamics simulation
• frame: time stamp at which the frame was extracted in ns

The folders contain the topologies (topol.top), topology include files (.itp), extracted structure file (frame_XXns.gro) and run input files sufficient to restart the simulation (md.tpr). The ConAn subfolder contains contact matricies for each analyzed time step (1 ns intervals).

PCA

This folder contains the results of and all files necesarry to replicate the principal component analysis of kinase domain dynamics.

• autocorrelation.svg: autocorrelations of the projections of the seperate simulation trajectories onto the first principal component
• average.pdb: average structure obtained during covariance analysis using gmx covar
• bb-traj_combined.xtc: combined simulation trajectories from all model and replicate simulations (seperate trajectories stored as traj_{model}_{rep}.xtc as described below)
• covar.txt: log file written during gmx covar analysis
• eigenval.xvg, eigenvec.trr: files containing the eigenvalues and eigenvectors, respectively, obtaining during the covariance analysis using gmx covar
• extreme_{model}_{rep}.pdb: structure files showing the two extreme projections along a simulation trajectory. files are labeled by Abl model and replicate number
• KD_noIa_bb_ref.pdb: reference structure for the kinase backbone atoms needed for analysis with gmx covar and anaeig
• modevectors_active-kinked_extreme.pse: pymol session file, which generated the porcupine plots described below
• PCA_KDdyn_PC1_1av: raw values (.csv files) and plots (.svg files) of the projection of the trajectories onto the first principal component when averaging across the whole trajectory
• PCA_KDdyn_PC1_ex100av400: raw values (.csv files) and plots (.svg files) of the projection of the trajectories onto the first principal component when averaging across blocks of 400 ns length while leaving out 100 ns in between the averaging blocks
• PCA_KDdyn_PC1-3: plot of the projection of the trajectories onto the first three principal components
• PCA_KDdyn_Pvals.csv: list of all p-values calculated for the projections onto the first 3 principal components (PC) of the different model simulations. To evaluate the robustnest of the p-values and the impact of correlation between the data points, the p-values were obtained on different bases:
  • all: all data points
  • discardXX: discard the first XX ns of each simulation
  • av: averaging across all data points (1av) or across time blocks of XX ns length (avXX)
  • exYYavXX: averaging across blocks of XX ns length, while excluding XX ns in between the blocks
  • everyXX: using a datapoint every XX ns, discarding the rest
• porcupine_{model}.png: porcupine plots for a kinase model with a kinked alpha_I helix and an active kinase model, both seperate and in comparison of the two models. the porcupine plots are obtained by reading the extreme projections of the model simulation trajectories with the modevectors.py script (https://pymolwiki.org/index.php/Modevectors)
• proj.xvg: projection of the combined trajectory onto the eigenvectors including the first 6 principal components
• proj_{model}_{rep}.xvg: projection of single trajectories onto the eigenvectors of the combined trajectory. the files are labeled by Abl model and replicate number
• steps: description of the steps performed during PCA including all Gromacs analysis commands and generation of porcupine plots
• traj_{model}_{rep}.xtc: simulation trajectory files containing the backbone atoms of the kinase domains, one frame written every 2 ns

setup_analysis

• analysis_Fig1-B-E.sh: Gromacs commands used to analyze kinase RMSD and RMSF and create the suitable index groups
• eq_sim_setup_steps.txt: Gromacs commands used to setup the equilibrium simulations for each Abl model. Steps included topology generation, building the structure files, solvating and ionizing the simulation system, and energy minimization

Umbrella

This folder contains the files needed to replicate the Umbrella Sampling simulations and Free Energy calculations of Myr unbinding.

• There a folders for SH3-SH2-kinase Abl models with different alpha_I helix conformations and for the membrane. Folders are named by the helix conformation or membrane in case of the membrane. alphaI-kink means the helix is in a kinked conformation as found in SH3-SH2-kinase crystal stuctures, alphaI-straight and alphaI-unfold means the helix assumes a straight or partially unfolded conformation as obtained by the Metadynamics simulations, and delta-alphaIb means that the helix was truncated starting at residue 518. These folders contain subfolders for equilibration, pulling and Umbrella Sampling simulations.
  • eq: equilibrium simulations started from Metadynamics frames to relax the structures in the absence of the Metadynamics bias. The included files are structure files (.gro), the topology (topol_sys.top) and topology include files (.itp), simulation parameters for energy minimization, NVT and NPT equilibration (.mdp), and the corresponding simulation start files (.tpr). The structure files include the extracted protein (protein.gro), myristoylated glycine (GLYM.gro), ATP (ATP.gro) and MG (MG.gro). The protein with the afore listed cofactors (system.gro) in its simulation box (system_box.gro) with the solvent (system_solv.gro) and neutralizing ions (system_solv_ions.gro) added and after energy minimization (system_em.gro). Subfolders for each simulation replicate (numbered) contain the simulation start file (md.tpr) for each run.
  • pull: simulations pulling Myr from its protein binding site or the membrane to accelerate the unbinding event. Simulation parameter and topology files are descibed above. Additionally the pulling parameters are included (pull_md.mdp). Numbered subfolders for each simulation replicate contain the last frame from the respective equilibrium simulation (eq_md.gro), and simulation start files for energy minimization (pull_em.tpr), equilibration (nvt.tpr and npt.tpr) and pulling simulation at the two different velocities 0.1 m/s and 0.05 m/s (pull_md_0.1ms.tpr and pull_md_0.05ms.tpr, respectively).
  • umbrella: simulations of the Umbrella Sampling windows and their analysis.
    • {rep}_{velocity}_{frame}_pullx.xvg: distances between the Myr binding site and Myr (collective variable) over time for each Umbrella Sampling window. Files are named by replicate number corresponding to the replicate numbers of equilibrium and pulling simulations, pulling velocity (1 for 0.1 m/s and 05 for 0.05 m/s), and frame number of the extracted frame that was used for the respective Umbrella Sampling window.
    • {rep}_{velocity}_{frame}.tpr: simulation start file for each Umbrella Sampling window, named equivalently to the distance files described above
    • analyze_umbrella_blocks.sh: bash script to perform the block analysis to assess convergence of the Umbrella Sampling simulations
    • analyze_umbrella_final.sh: Gromacs command used for the final PMF calculation using PMF wham
    • bsProfs_{start}-{end}ns.xvg: PMF profiles for each bootstrap along the distance collective variable, provided for each block and for the final analysis including simulation time 80-200 ns. Blocks are labeled by their start and end time in ns.
    • bsResult_{start}-{end}ns.xvg: average PMF profile and standard deviation obtained through bootstrapping.
    • frames.dat: list of frames all extracted frames used to start Umbrella Sampling simulations
    • histo_{start}-{end}.xvg: histograms showing coverage across the distance collective variable
    • profile_{start}-{end}.xvg: average PMF profiles over the diatnce between Myr and its binding site
    • pullx_files.xvg, tpr_files: list of the distance and simulation start files of all Umbrella Sampling windows, needed for gmx wham analysis
• Abl_Myr_pull_setup: text file including all Gromacs commands used to setup the simulations pulling Myr out of its protein binding site
• analyze_umbrella.sh: bash script used to run the weighted histogram analysis method (gmx wham) analysis
• start_umbrella.sh: bash script to automatically start the simulations of Umbrella Sampling windows
• umbrella_md.mdp: simulation parameters applied during the Umbrella Sampling windows
• umbrella_npt.mdp: simulation parameters applied while equilibrating the extracted Umbrella Sampling frames
• umbrella_sampling steps: text file listing the steps performed to extract frames from the Myr pulling simulations along the distance collective variable and setup the Umbrella Sampling simulations
• umbrella_submit.sh: submission script to run the Umbrella Sampling windows including equilibration

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Description of files used for each result figure in the accompanying publication (DOI: 10.7554/eLife.85216)

Fig 2:

In the folders for each Abl model:

• Simulation parameters
• .tpr files: start file for each simulation, can be used to replicate each simulation within machine precision
• .xvg files: raw numerical data for figure panels B, E
  • panel B: rmsf.xvg
  • panel E: rmsd_noIa_bb.xvg

'PCA' folder:

• raw data for panel C and D

Fig 3:

Data deposited in 'FDA' folder

• backbone trajectories (.xtc), FDA input parameters (input.pfi) and output (.pfr), force differences for visualization (diff* .pdb)

Fig 4:

Contact matrices for each time point in 'ConAn' subfolder

• native contacts stored in 'SH3-SH2-KD_noMyr' folder
• contacts after Metadnymics stored in 'Metadynamics/eq_after_metad' folder, subfolders are named by sigma (s), bias factor (bf), replicate (r) and timepoint of the extracted frame during Metadnymics (fr)

Fig 5:

Within 'Umbrella' folder for each Abl model:

• Simulation files for equilibration ('eq' folder) and pulling ('pull' folder) simulations: parameters .mdp, structure .gro, topologies .top/.itp, start file .tpr
• Simulation start files (.tpr) and force trace (* _pullf.xvg) for each sampling window, PMF trace and bootstraps as well as the histograms ('umbrella' folder)

Figure Supplements:

• Fig 1: file helicity.dat in folder for each Abl model
• Fig 3+4: additional FDA analysis, see main Fig 2
• Fig 5: KD-SH2_dist.xvg files in 'SH3-SH2-KD_noMyr' folder (panel A/equilibrium distance) and 'Metadnymics/metad' folder (panel B/Metadynamics distance, subfolders named by sigma, bias factor and replicate number)
• Fig 6: block analysis for main Fig 2
• Fig 7: same data as main Fig 2, seperated by Set
• Fig 8: block analysis for main Fig 5

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Directory tree

|-  README.md
+---FDA
|   \---FDA
|           diff_KD-whole_Myr.pfr
|           diff_KD-whole_Myr_graph_3-100.pdb
|           diff_KD-whole_Myr_graph_3-20.pdb
|           diff_KD-whole_Myr_graph_3-30.pdb
|           diff_KD-whole_Myr_graph_3-40.pdb
|           diff_KD-whole_Myr_graph_3-50.pdb
|           diff_KD-whole_Myr_graph_3-60.pdb
|           diff_KD-whole_Myr_graph_3-70.pdb
|           diff_KD-whole_Myr_graph_3-80.pdb
|           diff_KD-whole_Myr_graph_3-90.pdb
|           diff_KD-whole_Myr_graph_big-100.pdb
|           diff_KD-whole_Myr_graph_big-20.pdb
|           diff_KD-whole_Myr_graph_big-30.pdb
|           diff_KD-whole_Myr_graph_big-40.pdb
|           diff_KD-whole_Myr_graph_big-50.pdb
|           diff_KD-whole_Myr_graph_big-60.pdb
|           diff_KD-whole_Myr_graph_big-70.pdb
|           diff_KD-whole_Myr_graph_big-80.pdb
|           diff_KD-whole_Myr_graph_big-90.pdb
|           diff_KD-whole_noMyr.pfr
|           diff_KD-whole_noMyr_graph_3-100.pdb
|           diff_KD-whole_noMyr_graph_3-20.pdb
|           diff_KD-whole_noMyr_graph_3-30.pdb
|           diff_KD-whole_noMyr_graph_3-40.pdb
|           diff_KD-whole_noMyr_graph_3-50.pdb
|           diff_KD-whole_noMyr_graph_3-60.pdb
|           diff_KD-whole_noMyr_graph_3-70.pdb
|           diff_KD-whole_noMyr_graph_3-80.pdb
|           diff_KD-whole_noMyr_graph_3-90.pdb
|           diff_KD-whole_noMyr_graph_big-100.pdb
|           diff_KD-whole_noMyr_graph_big-20.pdb
|           diff_KD-whole_noMyr_graph_big-30.pdb
|           diff_KD-whole_noMyr_graph_big-40.pdb
|           diff_KD-whole_noMyr_graph_big-50.pdb
|           diff_KD-whole_noMyr_graph_big-60.pdb
|           diff_KD-whole_noMyr_graph_big-70.pdb
|           diff_KD-whole_noMyr_graph_big-80.pdb
|           diff_KD-whole_noMyr_graph_big-90.pdb
|           diff_kinked-straight_Myr.pfr
|           diff_kinked-straight_Myr_graph_3-100.pdb
|           diff_kinked-straight_Myr_graph_3-20.pdb
|           diff_kinked-straight_Myr_graph_3-30.pdb
|           diff_kinked-straight_Myr_graph_3-40.pdb
|           diff_kinked-straight_Myr_graph_3-50.pdb
|           diff_kinked-straight_Myr_graph_3-60.pdb
|           diff_kinked-straight_Myr_graph_3-70.pdb
|           diff_kinked-straight_Myr_graph_3-80.pdb
|           diff_kinked-straight_Myr_graph_3-90.pdb
|           diff_kinked-straight_Myr_graph_big-100.pdb
|           diff_kinked-straight_Myr_graph_big-20.pdb
|           diff_kinked-straight_Myr_graph_big-30.pdb
|           diff_kinked-straight_Myr_graph_big-40.pdb
|           diff_kinked-straight_Myr_graph_big-50.pdb
|           diff_kinked-straight_Myr_graph_big-60.pdb
|           diff_kinked-straight_Myr_graph_big-70.pdb
|           diff_kinked-straight_Myr_graph_big-80.pdb
|           diff_kinked-straight_Myr_graph_big-90.pdb
|           diff_kinked-straight_noMyr.pfr
|           diff_kinked-straight_noMyr_graph_3-100.pdb
|           diff_kinked-straight_noMyr_graph_3-20.pdb
|           diff_kinked-straight_noMyr_graph_3-30.pdb
|           diff_kinked-straight_noMyr_graph_3-40.pdb
|           diff_kinked-straight_noMyr_graph_3-50.pdb
|           diff_kinked-straight_noMyr_graph_3-60.pdb
|           diff_kinked-straight_noMyr_graph_3-70.pdb
|           diff_kinked-straight_noMyr_graph_3-80.pdb
|           diff_kinked-straight_noMyr_graph_3-90.pdb
|           diff_kinked-straight_noMyr_graph_big-100.pdb
|           diff_kinked-straight_noMyr_graph_big-20.pdb
|           diff_kinked-straight_noMyr_graph_big-30.pdb
|           diff_kinked-straight_noMyr_graph_big-40.pdb
|           diff_kinked-straight_noMyr_graph_big-50.pdb
|           diff_kinked-straight_noMyr_graph_big-60.pdb
|           diff_kinked-straight_noMyr_graph_big-70.pdb
|           diff_kinked-straight_noMyr_graph_big-80.pdb
|           diff_kinked-straight_noMyr_graph_big-90.pdb
|           diff_kinkedMyr-straightnoMyr.pfr
|           diff_kinkedMyr-straightnoMyr_graph_3-100.pdb
|           diff_kinkedMyr-straightnoMyr_graph_3-20.pdb
|           diff_kinkedMyr-straightnoMyr_graph_3-30.pdb
|           diff_kinkedMyr-straightnoMyr_graph_3-40.pdb
|           diff_kinkedMyr-straightnoMyr_graph_3-50.pdb
|           diff_kinkedMyr-straightnoMyr_graph_3-60.pdb
|           diff_kinkedMyr-straightnoMyr_graph_3-70.pdb
|           diff_kinkedMyr-straightnoMyr_graph_3-80.pdb
|           diff_kinkedMyr-straightnoMyr_graph_3-90.pdb
|           diff_Myr-noMyr_kinked.pfr
|           diff_Myr-noMyr_kinked_graph_3-100.pdb
|           diff_Myr-noMyr_kinked_graph_3-20.pdb
|           diff_Myr-noMyr_kinked_graph_3-30.pdb
|           diff_Myr-noMyr_kinked_graph_3-40.pdb
|           diff_Myr-noMyr_kinked_graph_3-50.pdb
|           diff_Myr-noMyr_kinked_graph_3-60.pdb
|           diff_Myr-noMyr_kinked_graph_3-70.pdb
|           diff_Myr-noMyr_kinked_graph_3-80.pdb
|           diff_Myr-noMyr_kinked_graph_3-90.pdb
|           diff_Myr-noMyr_kinked_graph_big-100.pdb
|           diff_Myr-noMyr_kinked_graph_big-20.pdb
|           diff_Myr-noMyr_kinked_graph_big-30.pdb
|           diff_Myr-noMyr_kinked_graph_big-40.pdb
|           diff_Myr-noMyr_kinked_graph_big-50.pdb
|           diff_Myr-noMyr_kinked_graph_big-60.pdb
|           diff_Myr-noMyr_kinked_graph_big-70.pdb
|           diff_Myr-noMyr_kinked_graph_big-80.pdb
|           diff_Myr-noMyr_kinked_graph_big-90.pdb
|           diff_Myr-noMyr_straight.pfr
|           diff_Myr-noMyr_straight_graph_3-100.pdb
|           diff_Myr-noMyr_straight_graph_3-20.pdb
|           diff_Myr-noMyr_straight_graph_3-30.pdb
|           diff_Myr-noMyr_straight_graph_3-40.pdb
|           diff_Myr-noMyr_straight_graph_3-50.pdb
|           diff_Myr-noMyr_straight_graph_3-60.pdb
|           diff_Myr-noMyr_straight_graph_3-70.pdb
|           diff_Myr-noMyr_straight_graph_3-80.pdb
|           diff_Myr-noMyr_straight_graph_3-90.pdb
|           diff_Myr-noMyr_straight_graph_big-100.pdb
|           diff_Myr-noMyr_straight_graph_big-20.pdb
|           diff_Myr-noMyr_straight_graph_big-30.pdb
|           diff_Myr-noMyr_straight_graph_big-40.pdb
|           diff_Myr-noMyr_straight_graph_big-50.pdb
|           diff_Myr-noMyr_straight_graph_big-60.pdb
|           diff_Myr-noMyr_straight_graph_big-70.pdb
|           diff_Myr-noMyr_straight_graph_big-80.pdb
|           diff_Myr-noMyr_straight_graph_big-90.pdb
|           diff_Myr-noMyr_whole-full.pfr
|           diff_Myr-noMyr_whole_graph_3-100.pdb
|           diff_Myr-noMyr_whole_graph_3-20.pdb
|           diff_Myr-noMyr_whole_graph_3-30.pdb
|           diff_Myr-noMyr_whole_graph_3-40.pdb
|           diff_Myr-noMyr_whole_graph_3-50.pdb
|           diff_Myr-noMyr_whole_graph_3-60.pdb
|           diff_Myr-noMyr_whole_graph_3-70.pdb
|           diff_Myr-noMyr_whole_graph_3-80.pdb
|           diff_Myr-noMyr_whole_graph_3-90.pdb
|           diff_Myr-noMyr_whole_graph_big-100.pdb
|           diff_Myr-noMyr_whole_graph_big-20.pdb
|           diff_Myr-noMyr_whole_graph_big-30.pdb
|           diff_Myr-noMyr_whole_graph_big-40.pdb
|           diff_Myr-noMyr_whole_graph_big-50.pdb
|           diff_Myr-noMyr_whole_graph_big-60.pdb
|           diff_Myr-noMyr_whole_graph_big-70.pdb
|           diff_Myr-noMyr_whole_graph_big-80.pdb
|           diff_Myr-noMyr_whole_graph_big-90.pdb
|           FDA.ipynb
|           input.pfi
|           KD-whole_Myr_3_50-70-90pN_aochalky-t15.tga
|           KD-whole_Myr_big_30-40pN_aochalky-t15.tga
|           KD-whole_noMyr_3_50-70-90pN_aochalky-t15.tga
|           KD-whole_noMyr_big_30-40pN_aochalky-t15.tga
|           kinase_kinked_Myr.edr
|           kinase_kinked_Myr.gro
|           kinase_kinked_Myr.log
|           kinase_kinked_Myr.ndx
|           kinase_kinked_Myr.pfr
|           kinase_kinked_Myr.tpr
|           kinase_kinked_Myr.trr
|           kinase_kinked_Myr_11.xtc
|           kinase_kinked_Myr_12.xtc
|           kinase_kinked_Myr_13.xtc
|           kinase_kinked_Myr_14.xtc
|           kinase_kinked_Myr_15.xtc
|           kinase_kinked_Myr_16.xtc
|           kinase_kinked_Myr_17.xtc
|           kinase_kinked_Myr_18.xtc
|           kinase_kinked_Myr_19.xtc
|           kinase_kinked_Myr_20.xtc
|           kinase_kinked_Myr_21.xtc
|           kinase_kinked_Myr_22.xtc
|           kinase_kinked_Myr_23.xtc
|           kinase_kinked_Myr_24.xtc
|           kinase_kinked_Myr_25.xtc
|           kinase_kinked_Myr_26.xtc
|           kinase_kinked_Myr_27.xtc
|           kinase_kinked_Myr_28.xtc
|           kinase_kinked_Myr_29.xtc
|           kinase_kinked_Myr_30.xtc
|           kinase_kinked_Myr_concat.xtc
|           kinase_kinked_noMyr.edr
|           kinase_kinked_noMyr.gro
|           kinase_kinked_noMyr.log
|           kinase_kinked_noMyr.ndx
|           kinase_kinked_noMyr.pfr
|           kinase_kinked_noMyr.tpr
|           kinase_kinked_noMyr.trr
|           kinase_kinked_noMyr_11.xtc
|           kinase_kinked_noMyr_12.xtc
|           kinase_kinked_noMyr_13.xtc
|           kinase_kinked_noMyr_14.xtc
|           kinase_kinked_noMyr_15.xtc
|           kinase_kinked_noMyr_16.xtc
|           kinase_kinked_noMyr_17.xtc
|           kinase_kinked_noMyr_18.xtc
|           kinase_kinked_noMyr_19.xtc
|           kinase_kinked_noMyr_20.xtc
|           kinase_kinked_noMyr_21.xtc
|           kinase_kinked_noMyr_22.xtc
|           kinase_kinked_noMyr_23.xtc
|           kinase_kinked_noMyr_24.xtc
|           kinase_kinked_noMyr_25.xtc
|           kinase_kinked_noMyr_26.xtc
|           kinase_kinked_noMyr_27.xtc
|           kinase_kinked_noMyr_28.xtc
|           kinase_kinked_noMyr_29.xtc
|           kinase_kinked_noMyr_30.xtc
|           kinase_kinked_noMyr_concat.xtc
|           kinase_straight_Myr.edr
|           kinase_straight_Myr.gro
|           kinase_straight_Myr.log
|           kinase_straight_Myr.ndx
|           kinase_straight_Myr.pfr
|           kinase_straight_Myr.tpr
|           kinase_straight_Myr.trr
|           kinase_straight_Myr_11.xtc
|           kinase_straight_Myr_12.xtc
|           kinase_straight_Myr_13.xtc
|           kinase_straight_Myr_14.xtc
|           kinase_straight_Myr_15.xtc
|           kinase_straight_Myr_16.xtc
|           kinase_straight_Myr_17.xtc
|           kinase_straight_Myr_18.xtc
|           kinase_straight_Myr_19.xtc
|           kinase_straight_Myr_20.xtc
|           kinase_straight_Myr_21.xtc
|           kinase_straight_Myr_22.xtc
|           kinase_straight_Myr_23.xtc
|           kinase_straight_Myr_24.xtc
|           kinase_straight_Myr_25.xtc
|           kinase_straight_Myr_26.xtc
|           kinase_straight_Myr_27.xtc
|           kinase_straight_Myr_28.xtc
|           kinase_straight_Myr_29.xtc
|           kinase_straight_Myr_30.xtc
|           kinase_straight_Myr_concat.xtc
|           kinase_straight_noMyr.edr
|           kinase_straight_noMyr.gro
|           kinase_straight_noMyr.log
|           kinase_straight_noMyr.ndx
|           kinase_straight_noMyr.pfr
|           kinase_straight_noMyr.tpr
|           kinase_straight_noMyr.trr
|           kinase_straight_noMyr_11.xtc
|           kinase_straight_noMyr_12.xtc
|           kinase_straight_noMyr_13.xtc
|           kinase_straight_noMyr_14.xtc
|           kinase_straight_noMyr_15.xtc
|           kinase_straight_noMyr_16.xtc
|           kinase_straight_noMyr_17.xtc
|           kinase_straight_noMyr_18.xtc
|           kinase_straight_noMyr_19.xtc
|           kinase_straight_noMyr_20.xtc
|           kinase_straight_noMyr_21.xtc
|           kinase_straight_noMyr_22.xtc
|           kinase_straight_noMyr_23.xtc
|           kinase_straight_noMyr_24.xtc
|           kinase_straight_noMyr_25.xtc
|           kinase_straight_noMyr_26.xtc
|           kinase_straight_noMyr_27.xtc
|           kinase_straight_noMyr_28.xtc
|           kinase_straight_noMyr_29.xtc
|           kinase_straight_noMyr_30.xtc
|           kinase_straight_noMyr_concat.xtc
|           kinked-straight_Myr_3_50-70-90pN_aochalky-t15.tga
|           kinked-straight_noMyr_3_50-70-90pN_aochalky-t15.tga
|           Myr-noMyr_kinked_3_50-70-90pN_aochalky-t15.tga
|           Myr-noMyr_straight_3_50-70-90pN_aochalky-t15.tga
|           Myr-noMyr_whole-full_3_50-70-90pN_aochalky-t15.tga
|           SH3-SH2-KD_Myr.edr
|           SH3-SH2-KD_Myr.gro
|           SH3-SH2-KD_Myr.log
|           SH3-SH2-KD_Myr.ndx
|           SH3-SH2-KD_Myr.pfr
|           SH3-SH2-KD_Myr.tpr
|           SH3-SH2-KD_Myr.trr
|           SH3-SH2-KD_Myr_11.xtc
|           SH3-SH2-KD_Myr_12.xtc
|           SH3-SH2-KD_Myr_13.xtc
|           SH3-SH2-KD_Myr_14.xtc
|           SH3-SH2-KD_Myr_15.xtc
|           SH3-SH2-KD_Myr_16.xtc
|           SH3-SH2-KD_Myr_17.xtc
|           SH3-SH2-KD_Myr_18.xtc
|           SH3-SH2-KD_Myr_19.xtc
|           SH3-SH2-KD_Myr_20.xtc
|           SH3-SH2-KD_Myr_21.xtc
|           SH3-SH2-KD_Myr_22.xtc
|           SH3-SH2-KD_Myr_23.xtc
|           SH3-SH2-KD_Myr_24.xtc
|           SH3-SH2-KD_Myr_25.xtc
|           SH3-SH2-KD_Myr_26.xtc
|           SH3-SH2-KD_Myr_27.xtc
|           SH3-SH2-KD_Myr_28.xtc
|           SH3-SH2-KD_Myr_29.xtc
|           SH3-SH2-KD_Myr_30.xtc
|           SH3-SH2-KD_Myr_concat.xtc
|           SH3-SH2-KD_noMyr.edr
|           SH3-SH2-KD_noMyr.gro
|           SH3-SH2-KD_noMyr.log
|           SH3-SH2-KD_noMyr.ndx
|           SH3-SH2-KD_noMyr.pfr
|           SH3-SH2-KD_noMyr.tpr
|           SH3-SH2-KD_noMyr.trr
|           SH3-SH2-KD_noMyr_11.xtc
|           SH3-SH2-KD_noMyr_12.xtc
|           SH3-SH2-KD_noMyr_13.xtc
|           SH3-SH2-KD_noMyr_14.xtc
|           SH3-SH2-KD_noMyr_15.xtc
|           SH3-SH2-KD_noMyr_16.xtc
|           SH3-SH2-KD_noMyr_17.xtc
|           SH3-SH2-KD_noMyr_18.xtc
|           SH3-SH2-KD_noMyr_19.xtc
|           SH3-SH2-KD_noMyr_20.xtc
|           SH3-SH2-KD_noMyr_21.xtc
|           SH3-SH2-KD_noMyr_22.xtc
|           SH3-SH2-KD_noMyr_23.xtc
|           SH3-SH2-KD_noMyr_24.xtc
|           SH3-SH2-KD_noMyr_25.xtc
|           SH3-SH2-KD_noMyr_26.xtc
|           SH3-SH2-KD_noMyr_27.xtc
|           SH3-SH2-KD_noMyr_28.xtc
|           SH3-SH2-KD_noMyr_29.xtc
|           SH3-SH2-KD_noMyr_30.xtc
|           SH3-SH2-KD_noMyr_concat.xtc
|           start_fda.sh
|           steps
|           submit.sh
|           vis_diff_KD-whole_Myr_Fig1.tcl
|           vis_diff_KD-whole_noMyr_Fig1.tcl
|           vis_diff_kinked-straight_Myr_Fig1.tcl
|           vis_diff_kinked-straight_noMyr_Fig1.tcl
|           vis_diff_Myr-noMyr_kinked_Fig1.tcl
|           vis_diff_Myr-noMyr_straight_Fig1.tcl
|           vis_diff_Myr-noMyr_whole-full_Fig1.tcl
|           
+---ff
|   \---charmm36-mar2019.ff
|           atomtypes.atp
|           cmap.itp
|           ffbonded.itp
|           ffnonbonded.itp
|           forcefield.doc
|           forcefield.itp
|           gb.itp
|           ions.itp
|           merged.arn
|           merged.c.tdb
|           merged.hdb
|           merged.n.tdb
|           merged.r2b
|           merged.rtp
|           merged.vsd
|           nbfix.itp
|           old_c36_cmap.itp
|           spc.itp
|           spce.itp
|           tip3p.itp
|           tip4p.itp
|           watermodels.dat
|           
+---kinase_active
|   \---kinase_active
|       +---Set1
|       |   |   ATP.itp
|       |   |   MG.itp
|       |   |   npt.mdp
|       |   |   nvt.mdp
|       |   |   posre_ATP.itp
|       |   |   posre_MG.itp
|       |   |   posre_protein.itp
|       |   |   production_md.mdp
|       |   |   protein.itp
|       |   |   step6.0_minimization.mdp
|       |   |   system.gro
|       |   |   system_box.gro
|       |   |   system_em.gro
|       |   |   system_solv.gro
|       |   |   system_solv_ions.gro
|       |   |   topol.top
|       |   |   
|       |   +---11
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       
|       |   +---12
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       
|       |   +---13
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       
|       |   +---14
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       
|       |   +---15
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       
|       |   +---16
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       
|       |   +---17
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       
|       |   +---18
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       
|       |   +---19
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       
|       |   \---20
|       |           md.tpr
|       |           npt.tpr
|       |           nvt.tpr
|       |           
|       \---Set2
|           |   ATP.itp
|           |   MG.itp
|           |   npt.mdp
|           |   nvt.mdp
|           |   posre_ATP.itp
|           |   posre_MG.itp
|           |   posre_protein.itp
|           |   production_md.mdp
|           |   protein.itp
|           |   step6.0_minimization.mdp
|           |   system_em.gro
|           |   topol.top
|           |   
|           +---21
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       
|           +---22
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       
|           +---23
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       
|           +---24
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       
|           +---25
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       
|           +---26
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       
|           +---27
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       
|           +---28
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       
|           +---29
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       
|           \---30
|                   md.tpr
|                   npt.tpr
|                   nvt.tpr
|                   
+---kinase_kinked_Myr
|   \---kinase_kinked_Myr
|       +---Set1
|       |   |   ATP.itp
|       |   |   index.ndx
|       |   |   MG_ion.itp
|       |   |   MYR.itp
|       |   |   npt.mdp
|       |   |   nvt.mdp
|       |   |   posre_ATP.itp
|       |   |   posre_MG.itp
|       |   |   posre_MYR.itp
|       |   |   posre_protein.itp
|       |   |   production_md.mdp
|       |   |   protein.itp
|       |   |   system.gro
|       |   |   system_box.gro
|       |   |   system_em.gro
|       |   |   system_solv.gro
|       |   |   system_solv_ions.gro
|       |   |   topol.top
|       |   |   
|       |   +---11
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---12
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---13
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---14
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---15
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---16
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---17
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---18
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---19
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   \---20
|       |           helicity.dat
|       |           md.tpr
|       |           npt.tpr
|       |           nvt.tpr
|       |           rmsd_noIa_bb.xvg
|       |           rmsf.xvg
|       |           
|       \---Set2
|           |   ATP.itp
|           |   index.ndx
|           |   MG_ion.itp
|           |   MYR.itp
|           |   npt.mdp
|           |   nvt.mdp
|           |   posre_ATP.itp
|           |   posre_MG.itp
|           |   posre_MYR.itp
|           |   posre_protein.itp
|           |   production_md.mdp
|           |   protein.itp
|           |   system_em.gro
|           |   topol.top
|           |   
|           +---21
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---22
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---23
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---24
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---25
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---26
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---27
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---28
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---29
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           \---30
|                   helicity.dat
|                   md.tpr
|                   npt.tpr
|                   nvt.tpr
|                   rmsd_noIa_bb.xvg
|                   rmsf.xvg
|                   
+---kinase_kinked_noMyr
|   \---kinase_kinked_noMyr
|       +---Set1
|       |   |   ATP.itp
|       |   |   index.ndx
|       |   |   MG_ion.itp
|       |   |   npt.mdp
|       |   |   nvt.mdp
|       |   |   posre_ATP.itp
|       |   |   posre_MG.itp
|       |   |   posre_protein.itp
|       |   |   production_md.mdp
|       |   |   protein.itp
|       |   |   system.gro
|       |   |   system_box.gro
|       |   |   system_em.gro
|       |   |   system_solv.gro
|       |   |   system_solv_ions.gro
|       |   |   topol.top
|       |   |   
|       |   +---11
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---12
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---13
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---14
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---15
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---16
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---17
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---18
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---19
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   \---20
|       |           helicity.dat
|       |           md.tpr
|       |           npt.tpr
|       |           nvt.tpr
|       |           rmsd_noIa_bb.xvg
|       |           rmsf.xvg
|       |           
|       \---Set2
|           |   ATP.itp
|           |   index.ndx
|           |   MG_ion.itp
|           |   npt.mdp
|           |   nvt.mdp
|           |   posre_ATP.itp
|           |   posre_MG.itp
|           |   posre_protein.itp
|           |   production_md.mdp
|           |   protein.itp
|           |   system_em.gro
|           |   topol.top
|           |   
|           +---21
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---22
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---23
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---24
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---25
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---26
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---27
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---28
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---29
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           \---30
|                   helicity.dat
|                   md.tpr
|                   npt.tpr
|                   nvt.tpr
|                   rmsd_noIa_bb.xvg
|                   rmsf.xvg
|                   
+---kinase_straight_Myr
|   \---kinase_straight_Myr
|       +---Set1
|       |   |   ATP.itp
|       |   |   index.ndx
|       |   |   MG.itp
|       |   |   MYR.itp
|       |   |   npt.mdp
|       |   |   nvt.mdp
|       |   |   posre_ATP.itp
|       |   |   posre_MG.itp
|       |   |   posre_MYR.itp
|       |   |   posre_protein.itp
|       |   |   production_md.mdp
|       |   |   protein.itp
|       |   |   system.gro
|       |   |   system_box.gro
|       |   |   system_em.gro
|       |   |   system_solv.gro
|       |   |   system_solv_ions.gro
|       |   |   topol.top
|       |   |   
|       |   +---11
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---12
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---13
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---14
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---15
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---16
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---17
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---18
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---19
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   \---20
|       |           helicity.dat
|       |           md.tpr
|       |           npt.tpr
|       |           nvt.tpr
|       |           rmsd_noIa_bb.xvg
|       |           rmsf.xvg
|       |           
|       \---Set2
|           |   ATP.itp
|           |   index.ndx
|           |   MG.itp
|           |   MYR.itp
|           |   npt.mdp
|           |   nvt.mdp
|           |   posre_ATP.itp
|           |   posre_MG.itp
|           |   posre_MYR.itp
|           |   posre_protein.itp
|           |   production_md.mdp
|           |   protein.itp
|           |   system_em.gro
|           |   topol.top
|           |   
|           +---21
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---22
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---23
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---24
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---25
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---26
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---27
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---28
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---29
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           \---30
|                   helicity.dat
|                   md.tpr
|                   npt.tpr
|                   nvt.tpr
|                   rmsd_noIa_bb.xvg
|                   rmsf.xvg
|                   
+---kinase_straight_noMyr
|   \---kinase_straight_noMyr
|       +---Set1
|       |   |   ATP.itp
|       |   |   index.ndx
|       |   |   MG.itp
|       |   |   npt.mdp
|       |   |   nvt.mdp
|       |   |   posre_ATP.itp
|       |   |   posre_MG.itp
|       |   |   posre_protein.itp
|       |   |   production_md.mdp
|       |   |   protein.itp
|       |   |   system.gro
|       |   |   system_box.gro
|       |   |   system_em.gro
|       |   |   system_solv.gro
|       |   |   system_solv_ions.gro
|       |   |   topol.top
|       |   |   
|       |   +---11
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---12
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---13
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---14
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---15
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---16
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---17
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---18
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---19
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   \---20
|       |           helicity.dat
|       |           md.tpr
|       |           npt.tpr
|       |           nvt.tpr
|       |           rmsd_noIa_bb.xvg
|       |           rmsf.xvg
|       |           
|       \---Set2
|           |   ATP.itp
|           |   index.ndx
|           |   MG.itp
|           |   npt.mdp
|           |   nvt.mdp
|           |   posre_ATP.itp
|           |   posre_MG.itp
|           |   posre_protein.itp
|           |   production_md.mdp
|           |   protein.itp
|           |   system_em.gro
|           |   topol.top
|           |   
|           +---21
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---22
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---23
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---24
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---25
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---26
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---27
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---28
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---29
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           \---30
|                   helicity.dat
|                   md.tpr
|                   npt.tpr
|                   nvt.tpr
|                   rmsd_noIa_bb.xvg
|                   rmsf.xvg
|                   
+---Metadynamics
|   \---Metadynamics
|       +---eq_after_metad
|       |   |   npt_step1.mdp
|       |   |   npt_step2.mdp
|       |   |   npt_step3.mdp
|       |   |   nvt.mdp
|       |   |   production_md.mdp
|       |   |   step6.0_minimization.mdp
|       |   |   
|       |   +---s2_bf20_r1_fr140-72ns
|       |   |   |   ATP.itp
|       |   |   |   frame_140-72ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s2_bf20_r1_fr65-84ns
|       |   |   |   ATP.itp
|       |   |   |   frame_65-84ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s2_bf20_r1_fr85-60ns
|       |   |   |   ATP.itp
|       |   |   |   frame85-6ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00483.dat
|       |   |           00484.dat
|       |   |           00485.dat
|       |   |           
|       |   +---s2_bf30_r1_fr115-84ns
|       |   |   |   ATP.itp
|       |   |   |   frame_115-84ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s2_bf30_r1_fr59-88ns
|       |   |   |   ATP.itp
|       |   |   |   frame_59-88ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s2_bf30_r1_fr71-36ns
|       |   |   |   ATP.itp
|       |   |   |   frame_71-36ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s2_bf30_r1_fr88-52ns
|       |   |   |   ATP.itp
|       |   |   |   frame_88-52ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s3_bf20_r1_fr38-64ns
|       |   |   |   ATP.itp
|       |   |   |   frame_38-64ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s3_bf25_r2_fr212-12ns
|       |   |   |   ATP.itp
|       |   |   |   frame_212-12ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s3_bf25_r2_fr59-36ns
|       |   |   |   ATP.itp
|       |   |   |   frame_59-36ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s3_bf25_r3_fr13-40ns
|       |   |   |   ATP.itp
|       |   |   |   frame_13-40ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s3_bf25_r3_fr29-12ns
|       |   |   |   ATP.itp
|       |   |   |   frame_29-12ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s3_bf30_r1_fr11-68ns
|       |   |   |   ATP.itp
|       |   |   |   frame_11-68ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s3_bf30_r1_fr21-68ns
|       |   |   |   ATP.itp
|       |   |   |   frame_21-68ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s3_bf30_r1_fr24-32ns
|       |   |   |   ATP.itp
|       |   |   |   frame_24-32ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s3_bf30_r1_fr8-64ns
|       |   |   |   ATP.itp
|       |   |   |   frame_8-64ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s3_bf30_r2_fr255-48ns
|       |   |   |   ATP.itp
|       |   |   |   frame_255-48ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s3_bf30_r2_fr429-72ns
|       |   |   |   ATP.itp
|       |   |   |   frame_429-72ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s3_bf30_r3_fr172-68ns
|       |   |   |   ATP.itp
|       |   |   |   frame_172-68ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s3_bf30_r3_fr26-36ns
|       |   |   |   ATP.itp
|       |   |   |   frame_26-36ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s3_bf30_r4_fr29-60ns
|       |   |   |   ATP.itp
|       |   |   |   frame_29-60ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   +---s3_bf30_r5_fr374-88ns
|       |   |   |   ATP.itp
|       |   |   |   frame_374-88ns.gro
|       |   |   |   md.tpr
|       |   |   |   posre_ATP.itp
|       |   |   |   posre_protein.itp
|       |   |   |   protein.itp
|       |   |   |   system_em.tpr
|       |   |   |   topol.top
|       |   |   |   
|       |   |   \---ConAn
|       |   |           00000.dat
|       |   |           00001.dat
|       |   |           00002.dat
|       |   |           00003.dat
|       |   |           ...
|       |   |           00498.dat
|       |   |           00499.dat
|       |   |           00500.dat
|       |   |           
|       |   \---s3_bf30_r5_fr49-04ns
|       |       |   ATP.itp
|       |       |   frame_49-04ns.gro
|       |       |   md.tpr
|       |       |   posre_ATP.itp
|       |       |   posre_protein.itp
|       |       |   protein.itp
|       |       |   system_em.tpr
|       |       |   topol.top
|       |       |   
|       |       \---ConAn
|       |               00000.dat
|       |               00001.dat
|       |               00002.dat
|       |               00003.dat
|       |               ...
|       |               00498.dat
|       |               00499.dat
|       |               00500.dat
|       |               
|       \---metad
|           |   Abl_ref.pdb
|           |   Abl_start-frame.pdb
|           |   
|           +---s2
|           |   +---bf100
|           |   |       COLVAR
|           |   |       HILLS
|           |   |       KD-SH2_dist.xvg
|           |   |       md.tpr
|           |   |       plumed.dat
|           |   |       
|           |   +---bf20
|           |   |       COLVAR
|           |   |       HILLS
|           |   |       KD-SH2_dist.xvg
|           |   |       md.tpr
|           |   |       plumed.dat
|           |   |       
|           |   +---bf30
|           |   |       COLVAR
|           |   |       HILLS
|           |   |       KD-SH2_dist.xvg
|           |   |       md.tpr
|           |   |       plumed.dat
|           |   |       
|           |   \---bf60
|           |           COLVAR
|           |           HILLS
|           |           KD-SH2_dist.xvg
|           |           md.tpr
|           |           plumed.dat
|           |           
|           \---s3
|               +---bf20
|               |   |   plumed.dat
|               |   |   
|               |   +---1
|               |   |       COLVAR
|               |   |       HILLS
|               |   |       KD-SH2_dist.xvg
|               |   |       md.tpr
|               |   |       
|               |   \---2
|               |           COLVAR
|               |           HILLS
|               |           KD-SH2_dist.xvg
|               |           md.tpr
|               |           
|               +---bf25
|               |   |   plumed.dat
|               |   |   
|               |   +---1
|               |   |       COLVAR
|               |   |       HILLS
|               |   |       KD-SH2_dist.xvg
|               |   |       md.tpr
|               |   |       
|               |   +---2
|               |   |       COLVAR
|               |   |       HILLS
|               |   |       KD-SH2_dist.xvg
|               |   |       md.tpr
|               |   |       
|               |   \---3
|               |           COLVAR
|               |           HILLS
|               |           KD-SH2_dist.xvg
|               |           md.tpr
|               |           
|               \---bf30
|                   |   plumed.dat
|                   |   
|                   +---1
|                   |       COLVAR
|                   |       HILLS
|                   |       KD-SH2_dist.xvg
|                   |       md.tpr
|                   |       
|                   +---2
|                   |       COLVAR
|                   |       HILLS
|                   |       KD-SH2_dist.xvg
|                   |       md.tpr
|                   |       
|                   +---3
|                   |       COLVAR
|                   |       HILLS
|                   |       KD-SH2_dist.xvg
|                   |       md.tpr
|                   |       
|                   +---4
|                   |       COLVAR
|                   |       HILLS
|                   |       KD-SH2_dist.xvg
|                   |       md.tpr
|                   |       
|                   \---5
|                           COLVAR
|                           HILLS
|                           KD-SH2_dist.xvg
|                           md.tpr
|                           
+---PCA
|   \---PCA
|           autocorrelation.svg
|           average.pdb
|           bb-traj_combined.xtc
|           covar.log
|           eigenval.xvg
|           eigenvec.trr
|           extreme_active_11.pdb
|           extreme_active_12.pdb
|           extreme_active_13.pdb
|           extreme_active_14.pdb
|           extreme_active_15.pdb
|           extreme_active_16.pdb
|           extreme_active_17.pdb
|           extreme_active_18.pdb
|           extreme_active_19.pdb
|           extreme_active_20.pdb
|           extreme_active_21.pdb
|           extreme_active_22.pdb
|           extreme_active_23.pdb
|           extreme_active_24.pdb
|           extreme_active_25.pdb
|           extreme_active_26.pdb
|           extreme_active_27.pdb
|           extreme_active_28.pdb
|           extreme_active_29.pdb
|           extreme_active_30.pdb
|           extreme_kinked_Myr_11.pdb
|           extreme_kinked_Myr_12.pdb
|           extreme_kinked_Myr_13.pdb
|           extreme_kinked_Myr_14.pdb
|           extreme_kinked_Myr_15.pdb
|           extreme_kinked_Myr_16.pdb
|           extreme_kinked_Myr_17.pdb
|           extreme_kinked_Myr_18.pdb
|           extreme_kinked_Myr_19.pdb
|           extreme_kinked_Myr_20.pdb
|           extreme_kinked_Myr_21.pdb
|           extreme_kinked_Myr_22.pdb
|           extreme_kinked_Myr_23.pdb
|           extreme_kinked_Myr_24.pdb
|           extreme_kinked_Myr_25.pdb
|           extreme_kinked_Myr_26.pdb
|           extreme_kinked_Myr_27.pdb
|           extreme_kinked_Myr_28.pdb
|           extreme_kinked_Myr_29.pdb
|           extreme_kinked_Myr_30.pdb
|           extreme_kinked_noMyr_11.pdb
|           extreme_kinked_noMyr_12.pdb
|           extreme_kinked_noMyr_13.pdb
|           extreme_kinked_noMyr_14.pdb
|           extreme_kinked_noMyr_15.pdb
|           extreme_kinked_noMyr_16.pdb
|           extreme_kinked_noMyr_17.pdb
|           extreme_kinked_noMyr_18.pdb
|           extreme_kinked_noMyr_19.pdb
|           extreme_kinked_noMyr_20.pdb
|           extreme_kinked_noMyr_21.pdb
|           extreme_kinked_noMyr_22.pdb
|           extreme_kinked_noMyr_23.pdb
|           extreme_kinked_noMyr_24.pdb
|           extreme_kinked_noMyr_25.pdb
|           extreme_kinked_noMyr_26.pdb
|           extreme_kinked_noMyr_27.pdb
|           extreme_kinked_noMyr_28.pdb
|           extreme_kinked_noMyr_29.pdb
|           extreme_kinked_noMyr_30.pdb
|           extreme_straight_Myr_11.pdb
|           extreme_straight_Myr_12.pdb
|           extreme_straight_Myr_13.pdb
|           extreme_straight_Myr_14.pdb
|           extreme_straight_Myr_15.pdb
|           extreme_straight_Myr_16.pdb
|           extreme_straight_Myr_17.pdb
|           extreme_straight_Myr_18.pdb
|           extreme_straight_Myr_19.pdb
|           extreme_straight_Myr_20.pdb
|           extreme_straight_Myr_21.pdb
|           extreme_straight_Myr_22.pdb
|           extreme_straight_Myr_23.pdb
|           extreme_straight_Myr_24.pdb
|           extreme_straight_Myr_25.pdb
|           extreme_straight_Myr_26.pdb
|           extreme_straight_Myr_27.pdb
|           extreme_straight_Myr_28.pdb
|           extreme_straight_Myr_29.pdb
|           extreme_straight_Myr_30.pdb
|           extreme_straight_noMyr_11.pdb
|           extreme_straight_noMyr_12.pdb
|           extreme_straight_noMyr_13.pdb
|           extreme_straight_noMyr_14.pdb
|           extreme_straight_noMyr_15.pdb
|           extreme_straight_noMyr_16.pdb
|           extreme_straight_noMyr_17.pdb
|           extreme_straight_noMyr_18.pdb
|           extreme_straight_noMyr_19.pdb
|           extreme_straight_noMyr_20.pdb
|           extreme_straight_noMyr_21.pdb
|           extreme_straight_noMyr_22.pdb
|           extreme_straight_noMyr_23.pdb
|           extreme_straight_noMyr_24.pdb
|           extreme_straight_noMyr_25.pdb
|           extreme_straight_noMyr_26.pdb
|           extreme_straight_noMyr_27.pdb
|           extreme_straight_noMyr_28.pdb
|           extreme_straight_noMyr_29.pdb
|           extreme_straight_noMyr_30.pdb
|           extreme_whole_Myr_11.pdb
|           extreme_whole_Myr_12.pdb
|           extreme_whole_Myr_13.pdb
|           extreme_whole_Myr_14.pdb
|           extreme_whole_Myr_15.pdb
|           extreme_whole_Myr_16.pdb
|           extreme_whole_Myr_17.pdb
|           extreme_whole_Myr_18.pdb
|           extreme_whole_Myr_19.pdb
|           extreme_whole_Myr_20.pdb
|           extreme_whole_Myr_21.pdb
|           extreme_whole_Myr_22.pdb
|           extreme_whole_Myr_23.pdb
|           extreme_whole_Myr_24.pdb
|           extreme_whole_Myr_25.pdb
|           extreme_whole_Myr_26.pdb
|           extreme_whole_Myr_27.pdb
|           extreme_whole_Myr_28.pdb
|           extreme_whole_Myr_29.pdb
|           extreme_whole_Myr_30.pdb
|           extreme_whole_noMyr_11.pdb
|           extreme_whole_noMyr_12.pdb
|           extreme_whole_noMyr_13.pdb
|           extreme_whole_noMyr_14.pdb
|           extreme_whole_noMyr_15.pdb
|           extreme_whole_noMyr_16.pdb
|           extreme_whole_noMyr_17.pdb
|           extreme_whole_noMyr_18.pdb
|           extreme_whole_noMyr_19.pdb
|           extreme_whole_noMyr_20.pdb
|           extreme_whole_noMyr_21.pdb
|           extreme_whole_noMyr_22.pdb
|           extreme_whole_noMyr_23.pdb
|           extreme_whole_noMyr_24.pdb
|           extreme_whole_noMyr_25.pdb
|           extreme_whole_noMyr_26.pdb
|           extreme_whole_noMyr_27.pdb
|           extreme_whole_noMyr_28.pdb
|           extreme_whole_noMyr_29.pdb
|           extreme_whole_noMyr_30.pdb
|           KD_noIa_bb_ref.pdb
|           modevectors_active-kinked_extreme.pse
|           PCA_KDdyn_PC1-3.svg
|           PCA_KDdyn_PC1.svg
|           PCA_KDdyn_PC1_1av.csv
|           PCA_KDdyn_PC1_1av.svg
|           PCA_KDdyn_PC1_ex100av400.csv
|           PCA_KDdyn_PC1_ex100av400.svg
|           PCA_KDdyn_Pvals.csv
|           porcupine_active-kinked.png
|           porcupine_active.png
|           porcupine_kinked.png
|           proj.xvg
|           proj_active_11.xvg
|           proj_active_12.xvg
|           proj_active_13.xvg
|           proj_active_14.xvg
|           proj_active_15.xvg
|           proj_active_16.xvg
|           proj_active_17.xvg
|           proj_active_18.xvg
|           proj_active_19.xvg
|           proj_active_20.xvg
|           proj_active_21.xvg
|           proj_active_22.xvg
|           proj_active_23.xvg
|           proj_active_24.xvg
|           proj_active_25.xvg
|           proj_active_26.xvg
|           proj_active_27.xvg
|           proj_active_28.xvg
|           proj_active_29.xvg
|           proj_active_30.xvg
|           proj_kinked_Myr_11.xvg
|           proj_kinked_Myr_12.xvg
|           proj_kinked_Myr_13.xvg
|           proj_kinked_Myr_14.xvg
|           proj_kinked_Myr_15.xvg
|           proj_kinked_Myr_16.xvg
|           proj_kinked_Myr_17.xvg
|           proj_kinked_Myr_18.xvg
|           proj_kinked_Myr_19.xvg
|           proj_kinked_Myr_20.xvg
|           proj_kinked_Myr_21.xvg
|           proj_kinked_Myr_22.xvg
|           proj_kinked_Myr_23.xvg
|           proj_kinked_Myr_24.xvg
|           proj_kinked_Myr_25.xvg
|           proj_kinked_Myr_26.xvg
|           proj_kinked_Myr_27.xvg
|           proj_kinked_Myr_28.xvg
|           proj_kinked_Myr_29.xvg
|           proj_kinked_Myr_30.xvg
|           proj_kinked_noMyr_11.xvg
|           proj_kinked_noMyr_12.xvg
|           proj_kinked_noMyr_13.xvg
|           proj_kinked_noMyr_14.xvg
|           proj_kinked_noMyr_15.xvg
|           proj_kinked_noMyr_16.xvg
|           proj_kinked_noMyr_17.xvg
|           proj_kinked_noMyr_18.xvg
|           proj_kinked_noMyr_19.xvg
|           proj_kinked_noMyr_20.xvg
|           proj_kinked_noMyr_21.xvg
|           proj_kinked_noMyr_22.xvg
|           proj_kinked_noMyr_23.xvg
|           proj_kinked_noMyr_24.xvg
|           proj_kinked_noMyr_25.xvg
|           proj_kinked_noMyr_26.xvg
|           proj_kinked_noMyr_27.xvg
|           proj_kinked_noMyr_28.xvg
|           proj_kinked_noMyr_29.xvg
|           proj_kinked_noMyr_30.xvg
|           proj_straight_Myr_11.xvg
|           proj_straight_Myr_12.xvg
|           proj_straight_Myr_13.xvg
|           proj_straight_Myr_14.xvg
|           proj_straight_Myr_15.xvg
|           proj_straight_Myr_16.xvg
|           proj_straight_Myr_17.xvg
|           proj_straight_Myr_18.xvg
|           proj_straight_Myr_19.xvg
|           proj_straight_Myr_20.xvg
|           proj_straight_Myr_21.xvg
|           proj_straight_Myr_22.xvg
|           proj_straight_Myr_23.xvg
|           proj_straight_Myr_24.xvg
|           proj_straight_Myr_25.xvg
|           proj_straight_Myr_26.xvg
|           proj_straight_Myr_27.xvg
|           proj_straight_Myr_28.xvg
|           proj_straight_Myr_29.xvg
|           proj_straight_Myr_30.xvg
|           proj_straight_noMyr_11.xvg
|           proj_straight_noMyr_12.xvg
|           proj_straight_noMyr_13.xvg
|           proj_straight_noMyr_14.xvg
|           proj_straight_noMyr_15.xvg
|           proj_straight_noMyr_16.xvg
|           proj_straight_noMyr_17.xvg
|           proj_straight_noMyr_18.xvg
|           proj_straight_noMyr_19.xvg
|           proj_straight_noMyr_20.xvg
|           proj_straight_noMyr_21.xvg
|           proj_straight_noMyr_22.xvg
|           proj_straight_noMyr_23.xvg
|           proj_straight_noMyr_24.xvg
|           proj_straight_noMyr_25.xvg
|           proj_straight_noMyr_26.xvg
|           proj_straight_noMyr_27.xvg
|           proj_straight_noMyr_28.xvg
|           proj_straight_noMyr_29.xvg
|           proj_straight_noMyr_30.xvg
|           proj_whole_Myr_11.xvg
|           proj_whole_Myr_12.xvg
|           proj_whole_Myr_13.xvg
|           proj_whole_Myr_14.xvg
|           proj_whole_Myr_15.xvg
|           proj_whole_Myr_16.xvg
|           proj_whole_Myr_17.xvg
|           proj_whole_Myr_18.xvg
|           proj_whole_Myr_19.xvg
|           proj_whole_Myr_20.xvg
|           proj_whole_Myr_21.xvg
|           proj_whole_Myr_22.xvg
|           proj_whole_Myr_23.xvg
|           proj_whole_Myr_24.xvg
|           proj_whole_Myr_25.xvg
|           proj_whole_Myr_26.xvg
|           proj_whole_Myr_27.xvg
|           proj_whole_Myr_28.xvg
|           proj_whole_Myr_29.xvg
|           proj_whole_Myr_30.xvg
|           proj_whole_noMyr_11.xvg
|           proj_whole_noMyr_12.xvg
|           proj_whole_noMyr_13.xvg
|           proj_whole_noMyr_14.xvg
|           proj_whole_noMyr_15.xvg
|           proj_whole_noMyr_16.xvg
|           proj_whole_noMyr_17.xvg
|           proj_whole_noMyr_18.xvg
|           proj_whole_noMyr_19.xvg
|           proj_whole_noMyr_20.xvg
|           proj_whole_noMyr_21.xvg
|           proj_whole_noMyr_22.xvg
|           proj_whole_noMyr_23.xvg
|           proj_whole_noMyr_24.xvg
|           proj_whole_noMyr_25.xvg
|           proj_whole_noMyr_26.xvg
|           proj_whole_noMyr_27.xvg
|           proj_whole_noMyr_28.xvg
|           proj_whole_noMyr_29.xvg
|           proj_whole_noMyr_30.xvg
|           steps
|           traj_active_11.xtc
|           traj_active_12.xtc
|           traj_active_13.xtc
|           traj_active_14.xtc
|           traj_active_15.xtc
|           traj_active_16.xtc
|           traj_active_17.xtc
|           traj_active_18.xtc
|           traj_active_19.xtc
|           traj_active_20.xtc
|           traj_active_21.xtc
|           traj_active_22.xtc
|           traj_active_23.xtc
|           traj_active_24.xtc
|           traj_active_25.xtc
|           traj_active_26.xtc
|           traj_active_27.xtc
|           traj_active_28.xtc
|           traj_active_29.xtc
|           traj_active_30.xtc
|           traj_kinked_Myr_11.xtc
|           traj_kinked_Myr_12.xtc
|           traj_kinked_Myr_13.xtc
|           traj_kinked_Myr_14.xtc
|           traj_kinked_Myr_15.xtc
|           traj_kinked_Myr_16.xtc
|           traj_kinked_Myr_17.xtc
|           traj_kinked_Myr_18.xtc
|           traj_kinked_Myr_19.xtc
|           traj_kinked_Myr_20.xtc
|           traj_kinked_Myr_21.xtc
|           traj_kinked_Myr_22.xtc
|           traj_kinked_Myr_23.xtc
|           traj_kinked_Myr_24.xtc
|           traj_kinked_Myr_25.xtc
|           traj_kinked_Myr_26.xtc
|           traj_kinked_Myr_27.xtc
|           traj_kinked_Myr_28.xtc
|           traj_kinked_Myr_29.xtc
|           traj_kinked_Myr_30.xtc
|           traj_kinked_noMyr_11.xtc
|           traj_kinked_noMyr_12.xtc
|           traj_kinked_noMyr_13.xtc
|           traj_kinked_noMyr_14.xtc
|           traj_kinked_noMyr_15.xtc
|           traj_kinked_noMyr_16.xtc
|           traj_kinked_noMyr_17.xtc
|           traj_kinked_noMyr_18.xtc
|           traj_kinked_noMyr_19.xtc
|           traj_kinked_noMyr_20.xtc
|           traj_kinked_noMyr_21.xtc
|           traj_kinked_noMyr_22.xtc
|           traj_kinked_noMyr_23.xtc
|           traj_kinked_noMyr_24.xtc
|           traj_kinked_noMyr_25.xtc
|           traj_kinked_noMyr_26.xtc
|           traj_kinked_noMyr_27.xtc
|           traj_kinked_noMyr_28.xtc
|           traj_kinked_noMyr_29.xtc
|           traj_kinked_noMyr_30.xtc
|           traj_straight_Myr_11.xtc
|           traj_straight_Myr_12.xtc
|           traj_straight_Myr_13.xtc
|           traj_straight_Myr_14.xtc
|           traj_straight_Myr_15.xtc
|           traj_straight_Myr_16.xtc
|           traj_straight_Myr_17.xtc
|           traj_straight_Myr_18.xtc
|           traj_straight_Myr_19.xtc
|           traj_straight_Myr_20.xtc
|           traj_straight_Myr_21.xtc
|           traj_straight_Myr_22.xtc
|           traj_straight_Myr_23.xtc
|           traj_straight_Myr_24.xtc
|           traj_straight_Myr_25.xtc
|           traj_straight_Myr_26.xtc
|           traj_straight_Myr_27.xtc
|           traj_straight_Myr_28.xtc
|           traj_straight_Myr_29.xtc
|           traj_straight_Myr_30.xtc
|           traj_straight_noMyr_11.xtc
|           traj_straight_noMyr_12.xtc
|           traj_straight_noMyr_13.xtc
|           traj_straight_noMyr_14.xtc
|           traj_straight_noMyr_15.xtc
|           traj_straight_noMyr_16.xtc
|           traj_straight_noMyr_17.xtc
|           traj_straight_noMyr_18.xtc
|           traj_straight_noMyr_19.xtc
|           traj_straight_noMyr_20.xtc
|           traj_straight_noMyr_21.xtc
|           traj_straight_noMyr_22.xtc
|           traj_straight_noMyr_23.xtc
|           traj_straight_noMyr_24.xtc
|           traj_straight_noMyr_25.xtc
|           traj_straight_noMyr_26.xtc
|           traj_straight_noMyr_27.xtc
|           traj_straight_noMyr_28.xtc
|           traj_straight_noMyr_29.xtc
|           traj_straight_noMyr_30.xtc
|           traj_whole_Myr_11.xtc
|           traj_whole_Myr_12.xtc
|           traj_whole_Myr_13.xtc
|           traj_whole_Myr_14.xtc
|           traj_whole_Myr_15.xtc
|           traj_whole_Myr_16.xtc
|           traj_whole_Myr_17.xtc
|           traj_whole_Myr_18.xtc
|           traj_whole_Myr_19.xtc
|           traj_whole_Myr_20.xtc
|           traj_whole_Myr_21.xtc
|           traj_whole_Myr_22.xtc
|           traj_whole_Myr_23.xtc
|           traj_whole_Myr_24.xtc
|           traj_whole_Myr_25.xtc
|           traj_whole_Myr_26.xtc
|           traj_whole_Myr_27.xtc
|           traj_whole_Myr_28.xtc
|           traj_whole_Myr_29.xtc
|           traj_whole_Myr_30.xtc
|           traj_whole_noMyr_11.xtc
|           traj_whole_noMyr_12.xtc
|           traj_whole_noMyr_13.xtc
|           traj_whole_noMyr_14.xtc
|           traj_whole_noMyr_15.xtc
|           traj_whole_noMyr_16.xtc
|           traj_whole_noMyr_17.xtc
|           traj_whole_noMyr_18.xtc
|           traj_whole_noMyr_19.xtc
|           traj_whole_noMyr_20.xtc
|           traj_whole_noMyr_21.xtc
|           traj_whole_noMyr_22.xtc
|           traj_whole_noMyr_23.xtc
|           traj_whole_noMyr_24.xtc
|           traj_whole_noMyr_25.xtc
|           traj_whole_noMyr_26.xtc
|           traj_whole_noMyr_27.xtc
|           traj_whole_noMyr_28.xtc
|           traj_whole_noMyr_29.xtc
|           traj_whole_noMyr_30.xtc
|           
+---setup_analysis
|       analysis_Fig1-B-E.sh
|       eq_sim_setup_steps.txt
|       
+---SH3-SH2-KD_Myr
|   \---SH3-SH2-KD_Myr
|       +---Set1
|       |   |   ATP.itp
|       |   |   index.ndx
|       |   |   MG.itp
|       |   |   MYR.itp
|       |   |   npt.mdp
|       |   |   nvt.mdp
|       |   |   posre_ATP.itp
|       |   |   posre_MG.itp
|       |   |   posre_MYR.itp
|       |   |   posre_protein.itp
|       |   |   production_md.mdp
|       |   |   protein.itp
|       |   |   system.gro
|       |   |   system_box.gro
|       |   |   system_em.gro
|       |   |   system_solv.gro
|       |   |   system_solv_ions.gro
|       |   |   topol.top
|       |   |   
|       |   +---11
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---12
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---13
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---14
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---15
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---16
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---17
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---18
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---19
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   \---20
|       |           helicity.dat
|       |           md.tpr
|       |           npt.tpr
|       |           nvt.tpr
|       |           rmsd_noIa_bb.xvg
|       |           rmsf.xvg
|       |           
|       \---Set2
|           |   ATP.itp
|           |   index.ndx
|           |   MG.itp
|           |   MYR.itp
|           |   npt.mdp
|           |   nvt.mdp
|           |   posre_ATP.itp
|           |   posre_MG.itp
|           |   posre_MYR.itp
|           |   posre_protein.itp
|           |   production_md.mdp
|           |   protein.itp
|           |   system_em.gro
|           |   topol.top
|           |   
|           +---21
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---22
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---23
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---24
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---25
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---26
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---27
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---28
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---29
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           \---30
|                   helicity.dat
|                   md.tpr
|                   npt.tpr
|                   nvt.tpr
|                   rmsd_noIa_bb.xvg
|                   rmsf.xvg
|                   
+---SH3-SH2-KD_noMyr
|   \---SH3-SH2-KD_noMyr
|       +---ConAn
|       |   |   SH2-KD_av_contacts_reps.csv
|       |   |   SH2-KD_contacts_native.csv
|       |   |   SH2-KD_median_contacts_time.csv
|       |   |   
|       |   +---1
|       |   |       00000.dat
|       |   |       00001.dat
|       |   |       00002.dat
|       |   |       00003.dat
|       |   |       ...
|       |   |       02498.dat
|       |   |       02499.dat
|       |   |       02500.dat
|       |   |       KD-SH2_dist.xvg
|       |   |       
|       |   +---10
|       |   |       00000.dat
|       |   |       00001.dat
|       |   |       00002.dat
|       |   |       00003.dat
|       |   |       ...
|       |   |       02498.dat
|       |   |       02499.dat
|       |   |       02500.dat
|       |   |       KD-SH2_dist.xvg
|       |   |       
|       |   +---2
|       |   |       00000.dat
|       |   |       00001.dat
|       |   |       00002.dat
|       |   |       00003.dat
|       |   |       ...
|       |   |       02498.dat
|       |   |       02499.dat
|       |   |       02500.dat
|       |   |       KD-SH2_dist.xvg
|       |   |       
|       |   +---3
|       |   |       00000.dat
|       |   |       00001.dat
|       |   |       00002.dat
|       |   |       00003.dat
|       |   |       ...
|       |   |       02498.dat
|       |   |       02499.dat
|       |   |       02500.dat
|       |   |       KD-SH2_dist.xvg
|       |   |       
|       |   +---4
|       |   |       00000.dat
|       |   |       00001.dat
|       |   |       00002.dat
|       |   |       00003.dat
|       |   |       ...
|       |   |       02498.dat
|       |   |       02499.dat
|       |   |       02500.dat
|       |   |       KD-SH2_dist.xvg
|       |   |       
|       |   +---5
|       |   |       00000.dat
|       |   |       00001.dat
|       |   |       00002.dat
|       |   |       00003.dat
|       |   |       ...
|       |   |       02498.dat
|       |   |       02499.dat
|       |   |       02500.dat
|       |   |       KD-SH2_dist.xvg
|       |   |       
|       |   +---6
|       |   |       00000.dat
|       |   |       00001.dat
|       |   |       00002.dat
|       |   |       00003.dat
|       |   |       ...
|       |   |       02498.dat
|       |   |       02499.dat
|       |   |       02500.dat
|       |   |       KD-SH2_dist.xvg
|       |   |       
|       |   +---7
|       |   |       00000.dat
|       |   |       00001.dat
|       |   |       00002.dat
|       |   |       00003.dat
|       |   |       ...
|       |   |       02498.dat
|       |   |       02499.dat
|       |   |       02500.dat
|       |   |       KD-SH2_dist.xvg
|       |   |       
|       |   +---8
|       |   |       00000.dat
|       |   |       00001.dat
|       |   |       00002.dat
|       |   |       00003.dat
|       |   |       ...
|       |   |       02498.dat
|       |   |       02499.dat
|       |   |       02500.dat
|       |   |       KD-SH2_dist.xvg
|       |   |       
|       |   \---9
|       |           00000.dat
|       |           00001.dat
|       |           00002.dat
|       |           00003.dat
|       |           ...
|       |           02498.dat
|       |           02499.dat
|       |           02500.dat
|       |           KD-SH2_dist.xvg
|       |           
|       +---Set1
|       |   |   ATP.itp
|       |   |   index.ndx
|       |   |   MG.itp
|       |   |   npt.mdp
|       |   |   nvt.mdp
|       |   |   posre_ATP.itp
|       |   |   posre_MG.itp
|       |   |   posre_protein.itp
|       |   |   production_md.mdp
|       |   |   protein.itp
|       |   |   system.gro
|       |   |   system_box.gro
|       |   |   system_em.gro
|       |   |   system_solv.gro
|       |   |   system_solv_ions.gro
|       |   |   topol.top
|       |   |   
|       |   +---11
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---12
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---13
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---14
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---15
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---16
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---17
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---18
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   +---19
|       |   |       helicity.dat
|       |   |       md.tpr
|       |   |       npt.tpr
|       |   |       nvt.tpr
|       |   |       rmsd_noIa_bb.xvg
|       |   |       rmsf.xvg
|       |   |       
|       |   \---20
|       |           helicity.dat
|       |           md.tpr
|       |           npt.tpr
|       |           nvt.tpr
|       |           rmsd_noIa_bb.xvg
|       |           rmsf.xvg
|       |           
|       \---Set2
|           |   ATP.itp
|           |   index.ndx
|           |   MG.itp
|           |   npt.mdp
|           |   nvt.mdp
|           |   posre_ATP.itp
|           |   posre_MG.itp
|           |   posre_protein.itp
|           |   production_md.mdp
|           |   protein.itp
|           |   system_em.gro
|           |   topol.top
|           |   
|           +---21
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---22
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---23
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---24
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---25
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---26
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---27
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---28
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           +---29
|           |       helicity.dat
|           |       md.tpr
|           |       npt.tpr
|           |       nvt.tpr
|           |       rmsd_noIa_bb.xvg
|           |       rmsf.xvg
|           |       
|           \---30
|                   helicity.dat
|                   md.tpr
|                   npt.tpr
|                   nvt.tpr
|                   rmsd_noIa_bb.xvg
|                   rmsf.xvg
|                   
\---Umbrella
    \---Umbrella
        |   Abl_Myr_pull_setup
        |   analyze_umbrella.sh
        |   start_umbrella.sh
        |   umbrella_md.mdp
        |   umbrella_npt.mdp
        |   umbrella_sampling_steps
        |   umbrella_submit.sh
        |   
        +---alphaI-kink
        |   +---eq
        |   |   |   ATP.gro
        |   |   |   ATP.itp
        |   |   |   GLYM.gro
        |   |   |   GLYM.itp
        |   |   |   ionize.tpr
        |   |   |   mdout.mdp
        |   |   |   MG.gro
        |   |   |   npt.gro
        |   |   |   npt.mdp
        |   |   |   npt.tpr
        |   |   |   npt_prot.gro
        |   |   |   nvt.gro
        |   |   |   nvt.mdp
        |   |   |   nvt.tpr
        |   |   |   posre_ATP.itp
        |   |   |   posre_GLYM.itp
        |   |   |   posre_protein.itp
        |   |   |   protein.gro
        |   |   |   protein.itp
        |   |   |   step6.0_minimization.mdp
        |   |   |   system.gro
        |   |   |   system_box.gro
        |   |   |   system_em.gro
        |   |   |   system_em.tpr
        |   |   |   system_solv.gro
        |   |   |   system_solv_ions.gro
        |   |   |   topol_sys.top
        |   |   |   
        |   |   +---1
        |   |   |       md.tpr
        |   |   |       
        |   |   +---10
        |   |   |       md.tpr
        |   |   |       
        |   |   +---2
        |   |   |       md.tpr
        |   |   |       
        |   |   +---3
        |   |   |       md.tpr
        |   |   |       
        |   |   +---4
        |   |   |       md.tpr
        |   |   |       
        |   |   +---5
        |   |   |       md.tpr
        |   |   |       
        |   |   +---6
        |   |   |       md.tpr
        |   |   |       
        |   |   +---7
        |   |   |       md.tpr
        |   |   |       
        |   |   +---8
        |   |   |       md.tpr
        |   |   |       
        |   |   \---9
        |   |           md.tpr
        |   |           
        |   +---pull
        |   |   |   ATP.itp
        |   |   |   GLYM.itp
        |   |   |   mdout.mdp
        |   |   |   npt.mdp
        |   |   |   nvt.mdp
        |   |   |   posre_ATP.itp
        |   |   |   posre_GLYM.itp
        |   |   |   posre_protein.itp
        |   |   |   protein.itp
        |   |   |   pull_md.mdp
        |   |   |   step6.0_minimization.mdp
        |   |   |   topol.top
        |   |   |   
        |   |   +---1
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---2
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---3
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---5
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---6
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---7
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   \---8
        |   |           eq_md.gro
        |   |           npt.tpr
        |   |           nvt.tpr
        |   |           pull_em.tpr
        |   |           pull_md_0.05ms.tpr
        |   |           pull_md_0.1ms.tpr
        |   |           
        |   \---umbrella
        |           1_05_165.tpr
        |           1_05_165_pullx.xvg
        |           1_05_202.tpr
        |           1_05_202_pullx.xvg
        |           1_05_25.tpr
        |           1_05_25_pullx.xvg
        |           1_05_322.tpr
        |           1_05_322_pullx.xvg
        |           1_05_359.tpr
        |           1_05_359_pullx.xvg
        |           1_05_463.tpr
        |           1_05_463_pullx.xvg
        |           1_05_50.tpr
        |           1_05_50_pullx.xvg
        |           1_05_555.tpr
        |           1_05_555_pullx.xvg
        |           1_05_573.tpr
        |           1_05_573_pullx.xvg
        |           1_05_591.tpr
        |           1_05_591_pullx.xvg
        |           1_05_675.tpr
        |           1_05_675_pullx.xvg
        |           1_05_687.tpr
        |           1_05_687_pullx.xvg
        |           1_05_71.tpr
        |           1_05_71_pullx.xvg
        |           1_05_730.tpr
        |           1_05_730_pullx.xvg
        |           1_05_750.tpr
        |           1_05_750_pullx.xvg
        |           1_05_831.tpr
        |           1_05_831_pullx.xvg
        |           1_05_897.tpr
        |           1_05_897_pullx.xvg
        |           1_05_924.tpr
        |           1_05_924_pullx.xvg
        |           1_1_1.tpr
        |           1_1_132.tpr
        |           1_1_132_pullx.xvg
        |           1_1_1_pullx.xvg
        |           1_1_20.tpr
        |           1_1_20_pullx.xvg
        |           1_1_221.tpr
        |           1_1_221_pullx.xvg
        |           1_1_255.tpr
        |           1_1_255_pullx.xvg
        |           1_1_282.tpr
        |           1_1_282_pullx.xvg
        |           1_1_288.tpr
        |           1_1_288_pullx.xvg
        |           1_1_294.tpr
        |           1_1_294_pullx.xvg
        |           1_1_371.tpr
        |           1_1_371_pullx.xvg
        |           1_1_403.tpr
        |           1_1_403_pullx.xvg
        |           1_1_437.tpr
        |           1_1_437_pullx.xvg
        |           1_1_508.tpr
        |           1_1_508_pullx.xvg
        |           1_1_523.tpr
        |           1_1_523_pullx.xvg
        |           1_1_568.tpr
        |           1_1_568_pullx.xvg
        |           1_1_582.tpr
        |           1_1_582_pullx.xvg
        |           1_1_590.tpr
        |           1_1_590_pullx.xvg
        |           1_1_592.tpr
        |           1_1_592_pullx.xvg
        |           1_1_602.tpr
        |           1_1_602_pullx.xvg
        |           1_1_91.tpr
        |           1_1_91_pullx.xvg
        |           3_05_1028.tpr
        |           3_05_1028_pullx.xvg
        |           3_05_1085.tpr
        |           3_05_1085_pullx.xvg
        |           3_05_112.tpr
        |           3_05_112_pullx.xvg
        |           3_05_1189.tpr
        |           3_05_1189_pullx.xvg
        |           3_05_1210.tpr
        |           3_05_1210_pullx.xvg
        |           3_05_1336.tpr
        |           3_05_1336_pullx.xvg
        |           3_05_1444.tpr
        |           3_05_1444_pullx.xvg
        |           3_05_1477.tpr
        |           3_05_1477_pullx.xvg
        |           3_05_1544.tpr
        |           3_05_1544_pullx.xvg
        |           3_05_220.tpr
        |           3_05_220_pullx.xvg
        |           3_05_223.tpr
        |           3_05_223_pullx.xvg
        |           3_05_243.tpr
        |           3_05_243_pullx.xvg
        |           3_05_278.tpr
        |           3_05_278_pullx.xvg
        |           3_05_292.tpr
        |           3_05_292_pullx.xvg
        |           3_05_407.tpr
        |           3_05_407_pullx.xvg
        |           3_05_499.tpr
        |           3_05_499_pullx.xvg
        |           3_05_592.tpr
        |           3_05_592_pullx.xvg
        |           3_05_68.tpr
        |           3_05_68_pullx.xvg
        |           3_05_697.tpr
        |           3_05_697_pullx.xvg
        |           3_05_903.tpr
        |           3_05_903_pullx.xvg
        |           3_05_93.tpr
        |           3_05_93_pullx.xvg
        |           3_1_12.tpr
        |           3_1_124.tpr
        |           3_1_124_pullx.xvg
        |           3_1_12_pullx.xvg
        |           3_1_152.tpr
        |           3_1_152_pullx.xvg
        |           3_1_192.tpr
        |           3_1_192_pullx.xvg
        |           3_1_201.tpr
        |           3_1_201_pullx.xvg
        |           3_1_216.tpr
        |           3_1_216_pullx.xvg
        |           3_1_26.tpr
        |           3_1_26_pullx.xvg
        |           3_1_279.tpr
        |           3_1_279_pullx.xvg
        |           3_1_288.tpr
        |           3_1_288_pullx.xvg
        |           3_1_425.tpr
        |           3_1_425_pullx.xvg
        |           3_1_469.tpr
        |           3_1_469_pullx.xvg
        |           3_1_511.tpr
        |           3_1_511_pullx.xvg
        |           3_1_544.tpr
        |           3_1_544_pullx.xvg
        |           3_1_574.tpr
        |           3_1_574_pullx.xvg
        |           3_1_635.tpr
        |           3_1_635_pullx.xvg
        |           3_1_667.tpr
        |           3_1_667_pullx.xvg
        |           3_1_70.tpr
        |           3_1_701.tpr
        |           3_1_701_pullx.xvg
        |           3_1_70_pullx.xvg
        |           3_1_713.tpr
        |           3_1_713_pullx.xvg
        |           5_05_1015.tpr
        |           5_05_1015_pullx.xvg
        |           5_05_1084.tpr
        |           5_05_1084_pullx.xvg
        |           5_05_1093.tpr
        |           5_05_1093_pullx.xvg
        |           5_05_12.tpr
        |           5_05_1275.tpr
        |           5_05_1275_pullx.xvg
        |           5_05_12_pullx.xvg
        |           5_05_204.tpr
        |           5_05_204_pullx.xvg
        |           5_05_249.tpr
        |           5_05_249_pullx.xvg
        |           5_05_305.tpr
        |           5_05_305_pullx.xvg
        |           5_05_364.tpr
        |           5_05_364_pullx.xvg
        |           5_05_374.tpr
        |           5_05_374_pullx.xvg
        |           5_05_409.tpr
        |           5_05_409_pullx.xvg
        |           5_05_543.tpr
        |           5_05_543_pullx.xvg
        |           5_05_58.tpr
        |           5_05_58_pullx.xvg
        |           5_05_60.tpr
        |           5_05_603.tpr
        |           5_05_603_pullx.xvg
        |           5_05_60_pullx.xvg
        |           5_05_719.tpr
        |           5_05_719_pullx.xvg
        |           5_05_8.tpr
        |           5_05_801.tpr
        |           5_05_801_pullx.xvg
        |           5_05_8_pullx.xvg
        |           5_05_932.tpr
        |           5_05_932_pullx.xvg
        |           5_1_10.tpr
        |           5_1_104.tpr
        |           5_1_104_pullx.xvg
        |           5_1_10_pullx.xvg
        |           5_1_12.tpr
        |           5_1_12_pullx.xvg
        |           5_1_168.tpr
        |           5_1_168_pullx.xvg
        |           5_1_184.tpr
        |           5_1_184_pullx.xvg
        |           5_1_20.tpr
        |           5_1_20_pullx.xvg
        |           5_1_248.tpr
        |           5_1_248_pullx.xvg
        |           5_1_272.tpr
        |           5_1_272_pullx.xvg
        |           5_1_318.tpr
        |           5_1_318_pullx.xvg
        |           5_1_378.tpr
        |           5_1_378_pullx.xvg
        |           5_1_415.tpr
        |           5_1_415_pullx.xvg
        |           5_1_437.tpr
        |           5_1_437_pullx.xvg
        |           5_1_486.tpr
        |           5_1_486_pullx.xvg
        |           5_1_537.tpr
        |           5_1_537_pullx.xvg
        |           5_1_583.tpr
        |           5_1_583_pullx.xvg
        |           5_1_628.tpr
        |           5_1_628_pullx.xvg
        |           5_1_64.tpr
        |           5_1_64_pullx.xvg
        |           5_1_82.tpr
        |           5_1_82_pullx.xvg
        |           analyze_umbrella_blocks.sh
        |           analyze_umbrella_final.sh
        |           bsProfs_100-120ns.xvg
        |           bsProfs_120-140ns.xvg
        |           bsProfs_140-160ns.xvg
        |           bsProfs_160-180ns.xvg
        |           bsProfs_180-200ns.xvg
        |           bsProfs_20-40ns.xvg
        |           bsProfs_40-60ns.xvg
        |           bsProfs_60-80ns.xvg
        |           bsProfs_80-100ns.xvg
        |           bsProfs_80-200ns.xvg
        |           bsResult_100-120ns.xvg
        |           bsResult_120-140ns.xvg
        |           bsResult_140-160ns.xvg
        |           bsResult_160-180ns.xvg
        |           bsResult_180-200ns.xvg
        |           bsResult_20-40ns.xvg
        |           bsResult_40-60ns.xvg
        |           bsResult_60-80ns.xvg
        |           bsResult_80-100ns.xvg
        |           bsResult_80-200ns.xvg
        |           frames.dat
        |           histo_100-120ns.xvg
        |           histo_120-140ns.xvg
        |           histo_140-160ns.xvg
        |           histo_160-180ns.xvg
        |           histo_180-200ns.xvg
        |           histo_20-40ns.xvg
        |           histo_40-60ns.xvg
        |           histo_60-80ns.xvg
        |           histo_80-100ns.xvg
        |           histo_80-200ns.xvg
        |           profile_100-120ns.xvg
        |           profile_120-140ns.xvg
        |           profile_140-160ns.xvg
        |           profile_160-180ns.xvg
        |           profile_180-200ns.xvg
        |           profile_20-40ns.xvg
        |           profile_40-60ns.xvg
        |           profile_60-80ns.xvg
        |           profile_80-100ns.xvg
        |           profile_80-200ns.xvg
        |           pullx_files.dat
        |           tpr_files.dat
        |           
        +---alphaI-straight
        |   +---eq
        |   |   |   ATP.gro
        |   |   |   ATP.itp
        |   |   |   GLYM.gro
        |   |   |   GLYM.itp
        |   |   |   ionize.tpr
        |   |   |   md.tpr
        |   |   |   mdout.mdp
        |   |   |   MG.gro
        |   |   |   npt.gro
        |   |   |   npt.mdp
        |   |   |   npt.tpr
        |   |   |   nvt.gro
        |   |   |   nvt.mdp
        |   |   |   nvt.tpr
        |   |   |   posre_ATP.itp
        |   |   |   posre_GLYM.itp
        |   |   |   posre_protein.itp
        |   |   |   production_md.mdp
        |   |   |   protein.gro
        |   |   |   protein.itp
        |   |   |   step6.0_minimization.mdp
        |   |   |   system.gro
        |   |   |   system_box.gro
        |   |   |   system_em.gro
        |   |   |   system_em.tpr
        |   |   |   system_solv.gro
        |   |   |   system_solv_ions.gro
        |   |   |   topol_sys.top
        |   |   |   
        |   |   +---1
        |   |   |       md.tpr
        |   |   |       
        |   |   +---10
        |   |   |       md.tpr
        |   |   |       
        |   |   +---2
        |   |   |       md.tpr
        |   |   |       
        |   |   +---3
        |   |   |       md.tpr
        |   |   |       
        |   |   +---4
        |   |   |       md.tpr
        |   |   |       
        |   |   +---5
        |   |   |       md.tpr
        |   |   |       
        |   |   +---6
        |   |   |       md.tpr
        |   |   |       
        |   |   +---7
        |   |   |       md.tpr
        |   |   |       
        |   |   +---8
        |   |   |       md.tpr
        |   |   |       
        |   |   \---9
        |   |           md.tpr
        |   |           
        |   +---pull
        |   |   |   ATP.itp
        |   |   |   GLYM.itp
        |   |   |   npt.mdp
        |   |   |   nvt.mdp
        |   |   |   posre_ATP.itp
        |   |   |   posre_GLYM.itp
        |   |   |   posre_protein.itp
        |   |   |   protein.itp
        |   |   |   pull_md.mdp
        |   |   |   step6.0_minimization.mdp
        |   |   |   topol.top
        |   |   |   
        |   |   +---1
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---10
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---2
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---3
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---4
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---5
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---6
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---8
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   \---9
        |   |           eq_md.gro
        |   |           npt.tpr
        |   |           nvt.tpr
        |   |           pull_em.tpr
        |   |           pull_md_0.05ms.tpr
        |   |           pull_md_0.1ms.tpr
        |   |           
        |   \---umbrella
        |           1_05_1011.tpr
        |           1_05_1011_pullx.xvg
        |           1_05_110.tpr
        |           1_05_1107.tpr
        |           1_05_1107_pullx.xvg
        |           1_05_110_pullx.xvg
        |           1_05_1224.tpr
        |           1_05_1224_pullx.xvg
        |           1_05_1250.tpr
        |           1_05_1250_pullx.xvg
        |           1_05_1292.tpr
        |           1_05_1292_pullx.xvg
        |           1_05_1318.tpr
        |           1_05_1318_pullx.xvg
        |           1_05_1355.tpr
        |           1_05_1355_pullx.xvg
        |           1_05_1371.tpr
        |           1_05_1371_pullx.xvg
        |           1_05_1439.tpr
        |           1_05_1439_pullx.xvg
        |           1_05_1727.tpr
        |           1_05_1727_pullx.xvg
        |           1_05_173.tpr
        |           1_05_173_pullx.xvg
        |           1_05_1768.tpr
        |           1_05_1768_pullx.xvg
        |           1_05_1814.tpr
        |           1_05_1814_pullx.xvg
        |           1_05_1847.tpr
        |           1_05_1847_pullx.xvg
        |           1_05_205.tpr
        |           1_05_205_pullx.xvg
        |           1_05_251.tpr
        |           1_05_251_pullx.xvg
        |           1_05_254.tpr
        |           1_05_254_pullx.xvg
        |           1_05_288.tpr
        |           1_05_288_pullx.xvg
        |           1_05_309.tpr
        |           1_05_309_pullx.xvg
        |           1_05_463.tpr
        |           1_05_463_pullx.xvg
        |           1_05_73.tpr
        |           1_05_73_pullx.xvg
        |           1_05_918.tpr
        |           1_05_918_pullx.xvg
        |           1_05_978.tpr
        |           1_05_978_pullx.xvg
        |           1_05_99.tpr
        |           1_05_99_pullx.xvg
        |           1_1_134.tpr
        |           1_1_134_pullx.xvg
        |           1_1_203.tpr
        |           1_1_203_pullx.xvg
        |           1_1_234.tpr
        |           1_1_234_pullx.xvg
        |           1_1_302.tpr
        |           1_1_302_pullx.xvg
        |           1_1_376.tpr
        |           1_1_376_pullx.xvg
        |           1_1_38.tpr
        |           1_1_38_pullx.xvg
        |           1_1_41.tpr
        |           1_1_41_pullx.xvg
        |           1_1_429.tpr
        |           1_1_429_pullx.xvg
        |           1_1_461.tpr
        |           1_1_461_pullx.xvg
        |           1_1_529.tpr
        |           1_1_529_pullx.xvg
        |           1_1_558.tpr
        |           1_1_558_pullx.xvg
        |           1_1_590.tpr
        |           1_1_590_pullx.xvg
        |           1_1_627.tpr
        |           1_1_627_pullx.xvg
        |           1_1_655.tpr
        |           1_1_655_pullx.xvg
        |           1_1_735.tpr
        |           1_1_735_pullx.xvg
        |           1_1_778.tpr
        |           1_1_778_pullx.xvg
        |           1_1_812.tpr
        |           1_1_812_pullx.xvg
        |           1_1_836.tpr
        |           1_1_836_pullx.xvg
        |           1_1_885.tpr
        |           1_1_885_pullx.xvg
        |           1_1_900.tpr
        |           1_1_900_pullx.xvg
        |           1_1_92.tpr
        |           1_1_92_pullx.xvg
        |           2_05_1040.tpr
        |           2_05_1040_pullx.xvg
        |           2_05_1210.tpr
        |           2_05_1210_pullx.xvg
        |           2_05_1344.tpr
        |           2_05_1344_pullx.xvg
        |           2_05_1373.tpr
        |           2_05_1373_pullx.xvg
        |           2_05_1434.tpr
        |           2_05_1434_pullx.xvg
        |           2_05_1481.tpr
        |           2_05_1481_pullx.xvg
        |           2_05_1490.tpr
        |           2_05_1490_pullx.xvg
        |           2_05_1530.tpr
        |           2_05_1530_pullx.xvg
        |           2_05_1654.tpr
        |           2_05_1654_pullx.xvg
        |           2_05_1706.tpr
        |           2_05_1706_pullx.xvg
        |           2_05_1758.tpr
        |           2_05_1758_pullx.xvg
        |           2_05_1787.tpr
        |           2_05_1787_pullx.xvg
        |           2_05_187.tpr
        |           2_05_187_pullx.xvg
        |           2_05_1885.tpr
        |           2_05_1885_pullx.xvg
        |           2_05_191.tpr
        |           2_05_1915.tpr
        |           2_05_1915_pullx.xvg
        |           2_05_191_pullx.xvg
        |           2_05_1959.tpr
        |           2_05_1959_pullx.xvg
        |           2_05_207.tpr
        |           2_05_207_pullx.xvg
        |           2_05_2103.tpr
        |           2_05_2103_pullx.xvg
        |           2_05_245.tpr
        |           2_05_245_pullx.xvg
        |           2_05_374.tpr
        |           2_05_374_pullx.xvg
        |           2_05_424.tpr
        |           2_05_424_pullx.xvg
        |           2_05_509.tpr
        |           2_05_509_pullx.xvg
        |           2_05_573.tpr
        |           2_05_573_pullx.xvg
        |           2_05_775.tpr
        |           2_05_775_pullx.xvg
        |           2_05_905.tpr
        |           2_05_905_pullx.xvg
        |           2_1_100.tpr
        |           2_1_100_pullx.xvg
        |           2_1_105.tpr
        |           2_1_105_pullx.xvg
        |           2_1_131.tpr
        |           2_1_131_pullx.xvg
        |           2_1_156.tpr
        |           2_1_156_pullx.xvg
        |           2_1_190.tpr
        |           2_1_190_pullx.xvg
        |           2_1_266.tpr
        |           2_1_266_pullx.xvg
        |           2_1_469.tpr
        |           2_1_469_pullx.xvg
        |           2_1_512.tpr
        |           2_1_512_pullx.xvg
        |           2_1_551.tpr
        |           2_1_551_pullx.xvg
        |           2_1_584.tpr
        |           2_1_584_pullx.xvg
        |           2_1_597.tpr
        |           2_1_597_pullx.xvg
        |           2_1_633.tpr
        |           2_1_633_pullx.xvg
        |           2_1_651.tpr
        |           2_1_651_pullx.xvg
        |           2_1_679.tpr
        |           2_1_679_pullx.xvg
        |           2_1_706.tpr
        |           2_1_706_pullx.xvg
        |           2_1_714.tpr
        |           2_1_714_pullx.xvg
        |           2_1_758.tpr
        |           2_1_758_pullx.xvg
        |           2_1_768.tpr
        |           2_1_768_pullx.xvg
        |           2_1_783.tpr
        |           2_1_783_pullx.xvg
        |           2_1_837.tpr
        |           2_1_837_pullx.xvg
        |           2_1_925.tpr
        |           2_1_925_pullx.xvg
        |           2_1_927.tpr
        |           2_1_927_pullx.xvg
        |           2_1_971.tpr
        |           2_1_971_pullx.xvg
        |           2_1_994.tpr
        |           2_1_994_pullx.xvg
        |           3_05_1215.tpr
        |           3_05_1215_pullx.xvg
        |           3_05_1234.tpr
        |           3_05_1234_pullx.xvg
        |           3_05_1415.tpr
        |           3_05_1415_pullx.xvg
        |           3_05_1456.tpr
        |           3_05_1456_pullx.xvg
        |           3_05_1554.tpr
        |           3_05_1554_pullx.xvg
        |           3_05_156.tpr
        |           3_05_156_pullx.xvg
        |           3_05_162.tpr
        |           3_05_162_pullx.xvg
        |           3_05_1729.tpr
        |           3_05_1729_pullx.xvg
        |           3_05_1841.tpr
        |           3_05_1841_pullx.xvg
        |           3_05_1892.tpr
        |           3_05_1892_pullx.xvg
        |           3_05_1942.tpr
        |           3_05_1942_pullx.xvg
        |           3_05_197.tpr
        |           3_05_197_pullx.xvg
        |           3_05_2000.tpr
        |           3_05_2000_pullx.xvg
        |           3_05_2048.tpr
        |           3_05_2048_pullx.xvg
        |           3_05_2059.tpr
        |           3_05_2059_pullx.xvg
        |           3_05_2139.tpr
        |           3_05_2139_pullx.xvg
        |           3_05_2209.tpr
        |           3_05_2209_pullx.xvg
        |           3_05_2275.tpr
        |           3_05_2275_pullx.xvg
        |           3_05_243.tpr
        |           3_05_243_pullx.xvg
        |           3_05_342.tpr
        |           3_05_342_pullx.xvg
        |           3_05_360.tpr
        |           3_05_360_pullx.xvg
        |           3_05_450.tpr
        |           3_05_450_pullx.xvg
        |           3_05_596.tpr
        |           3_05_596_pullx.xvg
        |           3_05_63.tpr
        |           3_05_63_pullx.xvg
        |           3_05_719.tpr
        |           3_05_719_pullx.xvg
        |           3_05_764.tpr
        |           3_05_764_pullx.xvg
        |           3_05_922.tpr
        |           3_05_922_pullx.xvg
        |           3_1_1056.tpr
        |           3_1_1056_pullx.xvg
        |           3_1_1068.tpr
        |           3_1_1068_pullx.xvg
        |           3_1_1079.tpr
        |           3_1_1079_pullx.xvg
        |           3_1_1086.tpr
        |           3_1_1086_pullx.xvg
        |           3_1_1119.tpr
        |           3_1_1119_pullx.xvg
        |           3_1_121.tpr
        |           3_1_121_pullx.xvg
        |           3_1_183.tpr
        |           3_1_183_pullx.xvg
        |           3_1_21.tpr
        |           3_1_219.tpr
        |           3_1_219_pullx.xvg
        |           3_1_21_pullx.xvg
        |           3_1_290.tpr
        |           3_1_290_pullx.xvg
        |           3_1_315.tpr
        |           3_1_315_pullx.xvg
        |           3_1_321.tpr
        |           3_1_321_pullx.xvg
        |           3_1_334.tpr
        |           3_1_334_pullx.xvg
        |           3_1_355.tpr
        |           3_1_355_pullx.xvg
        |           3_1_382.tpr
        |           3_1_382_pullx.xvg
        |           3_1_429.tpr
        |           3_1_429_pullx.xvg
        |           3_1_530.tpr
        |           3_1_530_pullx.xvg
        |           3_1_60.tpr
        |           3_1_60_pullx.xvg
        |           3_1_670.tpr
        |           3_1_670_pullx.xvg
        |           3_1_688.tpr
        |           3_1_688_pullx.xvg
        |           3_1_703.tpr
        |           3_1_703_pullx.xvg
        |           3_1_732.tpr
        |           3_1_732_pullx.xvg
        |           3_1_780.tpr
        |           3_1_780_pullx.xvg
        |           3_1_828.tpr
        |           3_1_828_pullx.xvg
        |           3_1_901.tpr
        |           3_1_901_pullx.xvg
        |           3_1_934.tpr
        |           3_1_934_pullx.xvg
        |           3_1_968.tpr
        |           3_1_968_pullx.xvg
        |           6_05_103.tpr
        |           6_05_103_pullx.xvg
        |           6_05_1083.tpr
        |           6_05_1083_pullx.xvg
        |           6_05_1171.tpr
        |           6_05_1171_pullx.xvg
        |           6_05_1257.tpr
        |           6_05_1257_pullx.xvg
        |           6_05_1312.tpr
        |           6_05_1312_pullx.xvg
        |           6_05_1453.tpr
        |           6_05_1453_pullx.xvg
        |           6_05_1472.tpr
        |           6_05_1472_pullx.xvg
        |           6_05_156.tpr
        |           6_05_1565.tpr
        |           6_05_1565_pullx.xvg
        |           6_05_156_pullx.xvg
        |           6_05_1594.tpr
        |           6_05_1594_pullx.xvg
        |           6_05_1657.tpr
        |           6_05_1657_pullx.xvg
        |           6_05_1674.tpr
        |           6_05_1674_pullx.xvg
        |           6_05_1721.tpr
        |           6_05_1721_pullx.xvg
        |           6_05_1811.tpr
        |           6_05_1811_pullx.xvg
        |           6_05_1991.tpr
        |           6_05_1991_pullx.xvg
        |           6_05_2014.tpr
        |           6_05_2014_pullx.xvg
        |           6_05_286.tpr
        |           6_05_286_pullx.xvg
        |           6_05_305.tpr
        |           6_05_305_pullx.xvg
        |           6_05_343.tpr
        |           6_05_343_pullx.xvg
        |           6_05_388.tpr
        |           6_05_388_pullx.xvg
        |           6_05_457.tpr
        |           6_05_457_pullx.xvg
        |           6_05_589.tpr
        |           6_05_589_pullx.xvg
        |           6_05_812.tpr
        |           6_05_812_pullx.xvg
        |           6_05_838.tpr
        |           6_05_838_pullx.xvg
        |           6_05_982.tpr
        |           6_05_982_pullx.xvg
        |           6_05_998.tpr
        |           6_05_998_pullx.xvg
        |           6_1_1008.tpr
        |           6_1_1008_pullx.xvg
        |           6_1_13.tpr
        |           6_1_13_pullx.xvg
        |           6_1_169.tpr
        |           6_1_169_pullx.xvg
        |           6_1_189.tpr
        |           6_1_189_pullx.xvg
        |           6_1_266.tpr
        |           6_1_266_pullx.xvg
        |           6_1_320.tpr
        |           6_1_320_pullx.xvg
        |           6_1_402.tpr
        |           6_1_402_pullx.xvg
        |           6_1_500.tpr
        |           6_1_500_pullx.xvg
        |           6_1_57.tpr
        |           6_1_57_pullx.xvg
        |           6_1_603.tpr
        |           6_1_603_pullx.xvg
        |           6_1_619.tpr
        |           6_1_619_pullx.xvg
        |           6_1_631.tpr
        |           6_1_631_pullx.xvg
        |           6_1_710.tpr
        |           6_1_710_pullx.xvg
        |           6_1_738.tpr
        |           6_1_738_pullx.xvg
        |           6_1_745.tpr
        |           6_1_745_pullx.xvg
        |           6_1_774.tpr
        |           6_1_774_pullx.xvg
        |           6_1_839.tpr
        |           6_1_839_pullx.xvg
        |           6_1_845.tpr
        |           6_1_845_pullx.xvg
        |           6_1_894.tpr
        |           6_1_894_pullx.xvg
        |           6_1_934.tpr
        |           6_1_934_pullx.xvg
        |           6_1_95.tpr
        |           6_1_95_pullx.xvg
        |           6_1_990.tpr
        |           6_1_990_pullx.xvg
        |           6_1_998.tpr
        |           6_1_998_pullx.xvg
        |           8_05_0.tpr
        |           8_05_0_pullx.xvg
        |           8_05_1032.tpr
        |           8_05_1032_pullx.xvg
        |           8_05_1270.tpr
        |           8_05_1270_pullx.xvg
        |           8_05_1382.tpr
        |           8_05_1382_pullx.xvg
        |           8_05_1498.tpr
        |           8_05_1498_pullx.xvg
        |           8_05_1672.tpr
        |           8_05_1672_pullx.xvg
        |           8_05_1778.tpr
        |           8_05_1778_pullx.xvg
        |           8_05_1816.tpr
        |           8_05_1816_pullx.xvg
        |           8_05_1884.tpr
        |           8_05_1884_pullx.xvg
        |           8_05_1912.tpr
        |           8_05_1912_pullx.xvg
        |           8_05_1971.tpr
        |           8_05_1971_pullx.xvg
        |           8_05_198.tpr
        |           8_05_1983.tpr
        |           8_05_1983_pullx.xvg
        |           8_05_198_pullx.xvg
        |           8_05_1991.tpr
        |           8_05_1991_pullx.xvg
        |           8_05_2016.tpr
        |           8_05_2016_pullx.xvg
        |           8_05_2017.tpr
        |           8_05_2017_pullx.xvg
        |           8_05_209.tpr
        |           8_05_209_pullx.xvg
        |           8_05_2120.tpr
        |           8_05_2120_pullx.xvg
        |           8_05_2121.tpr
        |           8_05_2121_pullx.xvg
        |           8_05_2262.tpr
        |           8_05_2262_pullx.xvg
        |           8_05_2300.tpr
        |           8_05_2300_pullx.xvg
        |           8_05_2474.tpr
        |           8_05_2474_pullx.xvg
        |           8_05_269.tpr
        |           8_05_269_pullx.xvg
        |           8_05_342.tpr
        |           8_05_342_pullx.xvg
        |           8_05_38.tpr
        |           8_05_38_pullx.xvg
        |           8_05_478.tpr
        |           8_05_478_pullx.xvg
        |           8_05_626.tpr
        |           8_05_626_pullx.xvg
        |           8_05_769.tpr
        |           8_05_769_pullx.xvg
        |           8_05_78.tpr
        |           8_05_78_pullx.xvg
        |           8_05_852.tpr
        |           8_05_852_pullx.xvg
        |           8_1_0.tpr
        |           8_1_0_pullx.xvg
        |           8_1_1000.tpr
        |           8_1_1000_pullx.xvg
        |           8_1_1040.tpr
        |           8_1_1040_pullx.xvg
        |           8_1_1111.tpr
        |           8_1_1111_pullx.xvg
        |           8_1_1162.tpr
        |           8_1_1162_pullx.xvg
        |           8_1_1237.tpr
        |           8_1_1237_pullx.xvg
        |           8_1_1270.tpr
        |           8_1_1270_pullx.xvg
        |           8_1_1294.tpr
        |           8_1_1294_pullx.xvg
        |           8_1_133.tpr
        |           8_1_133_pullx.xvg
        |           8_1_221.tpr
        |           8_1_221_pullx.xvg
        |           8_1_293.tpr
        |           8_1_293_pullx.xvg
        |           8_1_311.tpr
        |           8_1_311_pullx.xvg
        |           8_1_32.tpr
        |           8_1_32_pullx.xvg
        |           8_1_382.tpr
        |           8_1_382_pullx.xvg
        |           8_1_493.tpr
        |           8_1_493_pullx.xvg
        |           8_1_526.tpr
        |           8_1_526_pullx.xvg
        |           8_1_6.tpr
        |           8_1_647.tpr
        |           8_1_647_pullx.xvg
        |           8_1_658.tpr
        |           8_1_658_pullx.xvg
        |           8_1_6_pullx.xvg
        |           8_1_793.tpr
        |           8_1_793_pullx.xvg
        |           8_1_822.tpr
        |           8_1_822_pullx.xvg
        |           8_1_855.tpr
        |           8_1_855_pullx.xvg
        |           8_1_929.tpr
        |           8_1_929_pullx.xvg
        |           8_1_95.tpr
        |           8_1_954.tpr
        |           8_1_954_pullx.xvg
        |           8_1_95_pullx.xvg
        |           8_1_961.tpr
        |           8_1_961_pullx.xvg
        |           8_1_970.tpr
        |           8_1_970_pullx.xvg
        |           analyze_umbrella_blocks.sh
        |           analyze_umbrella_final.sh
        |           bsProfs_100-120ns.xvg
        |           bsProfs_120ns-140ns.xvg
        |           bsProfs_140-160ns.xvg
        |           bsProfs_160-180ns.xvg
        |           bsProfs_180-200ns.xvg
        |           bsProfs_20-40ns.xvg
        |           bsProfs_40-60ns.xvg
        |           bsProfs_60-80ns.xvg
        |           bsProfs_80-100ns.xvg
        |           bsProfs_80-200ns.xvg
        |           bsResult_100-120ns.xvg
        |           bsResult_120-140ns.xvg
        |           bsResult_140-160ns.xvg
        |           bsResult_160-180ns.xvg
        |           bsResult_180-200ns.xvg
        |           bsResult_20-40ns.xvg
        |           bsResult_40-60ns.xvg
        |           bsResult_60-80ns.xvg
        |           bsResult_80-100ns.xvg
        |           bsResult_80-200ns.xvg
        |           frames.dat
        |           histo_100-120ns.xvg
        |           histo_120-140ns.xvg
        |           histo_140-160ns.xvg
        |           histo_160-180ns.xvg
        |           histo_180-200ns.xvg
        |           histo_20-40ns.xvg
        |           histo_40-60ns.xvg
        |           histo_60-80ns.xvg
        |           histo_80-100ns.xvg
        |           histo_80-200ns.xvg
        |           profile_100-120ns.xvg
        |           profile_120-140ns.xvg
        |           profile_140-160ns.xvg
        |           profile_160-180ns.xvg
        |           profile_180-200ns.xvg
        |           profile_20-40ns.xvg
        |           profile_40-60ns.xvg
        |           profile_60-80ns.xvg
        |           profile_80-100ns.xvg
        |           profile_80-200ns.xvg
        |           pullx_files.dat
        |           tpr_files.dat
        |           
        +---alphaI-unfold
        |   +---eq
        |   |   |   ATP.gro
        |   |   |   ATP.itp
        |   |   |   GLYM.gro
        |   |   |   GLYM.itp
        |   |   |   ionize.tpr
        |   |   |   md.tpr
        |   |   |   mdout.mdp
        |   |   |   MG.gro
        |   |   |   npt.gro
        |   |   |   npt.mdp
        |   |   |   npt.tpr
        |   |   |   nvt.gro
        |   |   |   nvt.mdp
        |   |   |   nvt.tpr
        |   |   |   posre_ATP.itp
        |   |   |   posre_GLYM.itp
        |   |   |   posre_protein.itp
        |   |   |   production_md.mdp
        |   |   |   protein.gro
        |   |   |   protein.itp
        |   |   |   step6.0_minimization.mdp
        |   |   |   system.gro
        |   |   |   system_box.gro
        |   |   |   system_em.gro
        |   |   |   system_em.tpr
        |   |   |   system_solv.gro
        |   |   |   system_solv_ions.gro
        |   |   |   topol_sys.top
        |   |   |   
        |   |   +---1
        |   |   |       md.tpr
        |   |   |       
        |   |   +---10
        |   |   |       md.tpr
        |   |   |       
        |   |   +---2
        |   |   |       md.tpr
        |   |   |       
        |   |   +---3
        |   |   |       md.tpr
        |   |   |       
        |   |   +---4
        |   |   |       md.tpr
        |   |   |       
        |   |   +---5
        |   |   |       md.tpr
        |   |   |       
        |   |   +---6
        |   |   |       md.tpr
        |   |   |       
        |   |   +---7
        |   |   |       md.tpr
        |   |   |       
        |   |   +---8
        |   |   |       md.tpr
        |   |   |       
        |   |   \---9
        |   |           md.tpr
        |   |           
        |   +---pull
        |   |   |   ATP.itp
        |   |   |   GLYM.itp
        |   |   |   npt.mdp
        |   |   |   nvt.mdp
        |   |   |   posre_ATP.itp
        |   |   |   posre_GLYM.itp
        |   |   |   posre_protein.itp
        |   |   |   protein.itp
        |   |   |   pull_md.mdp
        |   |   |   step6.0_minimization.mdp
        |   |   |   topol.top
        |   |   |   
        |   |   +---1
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---10
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---2
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---3
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---4
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---5
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---7
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---8
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   \---9
        |   |           eq_md.gro
        |   |           npt.tpr
        |   |           nvt.tpr
        |   |           pull_em.tpr
        |   |           pull_md_0.05ms.tpr
        |   |           pull_md_0.1ms.tpr
        |   |           
        |   \---umbrella
        |           10_05_1148.tpr
        |           10_05_1148_pullx.xvg
        |           10_05_1201.tpr
        |           10_05_1201_pullx.xvg
        |           10_05_1261.tpr
        |           10_05_1261_pullx.xvg
        |           10_05_1289.tpr
        |           10_05_1289_pullx.xvg
        |           10_05_1354.tpr
        |           10_05_1354_pullx.xvg
        |           10_05_1365.tpr
        |           10_05_1365_pullx.xvg
        |           10_05_1521.tpr
        |           10_05_1521_pullx.xvg
        |           10_05_1629.tpr
        |           10_05_1629_pullx.xvg
        |           10_05_1663.tpr
        |           10_05_1663_pullx.xvg
        |           10_05_1860.tpr
        |           10_05_1860_pullx.xvg
        |           10_05_1936.tpr
        |           10_05_1936_pullx.xvg
        |           10_05_196.tpr
        |           10_05_196_pullx.xvg
        |           10_05_334.tpr
        |           10_05_334_pullx.xvg
        |           10_05_34.tpr
        |           10_05_341.tpr
        |           10_05_341_pullx.xvg
        |           10_05_34_pullx.xvg
        |           10_05_382.tpr
        |           10_05_382_pullx.xvg
        |           10_05_653.tpr
        |           10_05_653_pullx.xvg
        |           10_05_753.tpr
        |           10_05_753_pullx.xvg
        |           10_05_803.tpr
        |           10_05_803_pullx.xvg
        |           10_05_968.tpr
        |           10_05_968_pullx.xvg
        |           10_05_997.tpr
        |           10_05_997_pullx.xvg
        |           10_1_100.tpr
        |           10_1_100_pullx.xvg
        |           10_1_103.tpr
        |           10_1_103_pullx.xvg
        |           10_1_124.tpr
        |           10_1_124_pullx.xvg
        |           10_1_13.tpr
        |           10_1_13_pullx.xvg
        |           10_1_198.tpr
        |           10_1_198_pullx.xvg
        |           10_1_309.tpr
        |           10_1_309_pullx.xvg
        |           10_1_348.tpr
        |           10_1_348_pullx.xvg
        |           10_1_376.tpr
        |           10_1_376_pullx.xvg
        |           10_1_419.tpr
        |           10_1_419_pullx.xvg
        |           10_1_501.tpr
        |           10_1_501_pullx.xvg
        |           10_1_552.tpr
        |           10_1_552_pullx.xvg
        |           10_1_576.tpr
        |           10_1_576_pullx.xvg
        |           10_1_686.tpr
        |           10_1_686_pullx.xvg
        |           10_1_693.tpr
        |           10_1_693_pullx.xvg
        |           10_1_70.tpr
        |           10_1_708.tpr
        |           10_1_708_pullx.xvg
        |           10_1_70_pullx.xvg
        |           10_1_778.tpr
        |           10_1_778_pullx.xvg
        |           10_1_785.tpr
        |           10_1_785_pullx.xvg
        |           10_1_792.tpr
        |           10_1_792_pullx.xvg
        |           10_1_839.tpr
        |           10_1_839_pullx.xvg
        |           10_1_878.tpr
        |           10_1_878_pullx.xvg
        |           10_1_88.tpr
        |           10_1_88_pullx.xvg
        |           10_1_897.tpr
        |           10_1_897_pullx.xvg
        |           10_1_931.tpr
        |           10_1_931_pullx.xvg
        |           10_1_977.tpr
        |           10_1_977_pullx.xvg
        |           1_05_105.tpr
        |           1_05_105_pullx.xvg
        |           1_05_1127.tpr
        |           1_05_1127_pullx.xvg
        |           1_05_1209.tpr
        |           1_05_1209_pullx.xvg
        |           1_05_1350.tpr
        |           1_05_1350_pullx.xvg
        |           1_05_1423.tpr
        |           1_05_1423_pullx.xvg
        |           1_05_1494.tpr
        |           1_05_1494_pullx.xvg
        |           1_05_1510.tpr
        |           1_05_1510_pullx.xvg
        |           1_05_1620.tpr
        |           1_05_1620_pullx.xvg
        |           1_05_1735.tpr
        |           1_05_1735_pullx.xvg
        |           1_05_1968.tpr
        |           1_05_1968_pullx.xvg
        |           1_05_2058.tpr
        |           1_05_2058_pullx.xvg
        |           1_05_2132.tpr
        |           1_05_2132_pullx.xvg
        |           1_05_2169.tpr
        |           1_05_2169_pullx.xvg
        |           1_05_241.tpr
        |           1_05_241_pullx.xvg
        |           1_05_299.tpr
        |           1_05_299_pullx.xvg
        |           1_05_32.tpr
        |           1_05_32_pullx.xvg
        |           1_05_370.tpr
        |           1_05_370_pullx.xvg
        |           1_05_410.tpr
        |           1_05_410_pullx.xvg
        |           1_05_524.tpr
        |           1_05_524_pullx.xvg
        |           1_05_664.tpr
        |           1_05_664_pullx.xvg
        |           1_05_769.tpr
        |           1_05_769_pullx.xvg
        |           1_05_871.tpr
        |           1_05_871_pullx.xvg
        |           1_05_998.tpr
        |           1_05_998_pullx.xvg
        |           1_1_0.tpr
        |           1_1_0_pullx.xvg
        |           1_1_1070.tpr
        |           1_1_1070_pullx.xvg
        |           1_1_109.tpr
        |           1_1_1093.tpr
        |           1_1_1093_pullx.xvg
        |           1_1_109_pullx.xvg
        |           1_1_266.tpr
        |           1_1_266_pullx.xvg
        |           1_1_456.tpr
        |           1_1_456_pullx.xvg
        |           1_1_512.tpr
        |           1_1_512_pullx.xvg
        |           1_1_58.tpr
        |           1_1_587.tpr
        |           1_1_587_pullx.xvg
        |           1_1_58_pullx.xvg
        |           1_1_628.tpr
        |           1_1_628_pullx.xvg
        |           1_1_661.tpr
        |           1_1_661_pullx.xvg
        |           1_1_692.tpr
        |           1_1_692_pullx.xvg
        |           1_1_7.tpr
        |           1_1_748.tpr
        |           1_1_748_pullx.xvg
        |           1_1_770.tpr
        |           1_1_770_pullx.xvg
        |           1_1_7_pullx.xvg
        |           1_1_823.tpr
        |           1_1_823_pullx.xvg
        |           1_1_849.tpr
        |           1_1_849_pullx.xvg
        |           1_1_908.tpr
        |           1_1_908_pullx.xvg
        |           1_1_996.tpr
        |           1_1_996_pullx.xvg
        |           2_05_109.tpr
        |           2_05_1093.tpr
        |           2_05_1093_pullx.xvg
        |           2_05_109_pullx.xvg
        |           2_05_1236.tpr
        |           2_05_1236_pullx.xvg
        |           2_05_1314.tpr
        |           2_05_1314_pullx.xvg
        |           2_05_133.tpr
        |           2_05_133_pullx.xvg
        |           2_05_1385.tpr
        |           2_05_1385_pullx.xvg
        |           2_05_1416.tpr
        |           2_05_1416_pullx.xvg
        |           2_05_1446.tpr
        |           2_05_1446_pullx.xvg
        |           2_05_1663.tpr
        |           2_05_1663_pullx.xvg
        |           2_05_168.tpr
        |           2_05_168_pullx.xvg
        |           2_05_1713.tpr
        |           2_05_1713_pullx.xvg
        |           2_05_1749.tpr
        |           2_05_1749_pullx.xvg
        |           2_05_1776.tpr
        |           2_05_1776_pullx.xvg
        |           2_05_186.tpr
        |           2_05_186_pullx.xvg
        |           2_05_1999.tpr
        |           2_05_1999_pullx.xvg
        |           2_05_2036.tpr
        |           2_05_2036_pullx.xvg
        |           2_05_2064.tpr
        |           2_05_2064_pullx.xvg
        |           2_05_224.tpr
        |           2_05_224_pullx.xvg
        |           2_05_235.tpr
        |           2_05_235_pullx.xvg
        |           2_05_25.tpr
        |           2_05_255.tpr
        |           2_05_255_pullx.xvg
        |           2_05_25_pullx.xvg
        |           2_05_268.tpr
        |           2_05_268_pullx.xvg
        |           2_05_337.tpr
        |           2_05_337_pullx.xvg
        |           2_05_799.tpr
        |           2_05_799_pullx.xvg
        |           2_05_961.tpr
        |           2_05_961_pullx.xvg
        |           2_05_982.tpr
        |           2_05_982_pullx.xvg
        |           2_1_1028.tpr
        |           2_1_1028_pullx.xvg
        |           2_1_107.tpr
        |           2_1_107_pullx.xvg
        |           2_1_187.tpr
        |           2_1_187_pullx.xvg
        |           2_1_216.tpr
        |           2_1_216_pullx.xvg
        |           2_1_253.tpr
        |           2_1_253_pullx.xvg
        |           2_1_269.tpr
        |           2_1_269_pullx.xvg
        |           2_1_361.tpr
        |           2_1_361_pullx.xvg
        |           2_1_517.tpr
        |           2_1_517_pullx.xvg
        |           2_1_612.tpr
        |           2_1_612_pullx.xvg
        |           2_1_65.tpr
        |           2_1_65_pullx.xvg
        |           2_1_670.tpr
        |           2_1_670_pullx.xvg
        |           2_1_673.tpr
        |           2_1_673_pullx.xvg
        |           2_1_732.tpr
        |           2_1_732_pullx.xvg
        |           2_1_762.tpr
        |           2_1_762_pullx.xvg
        |           2_1_815.tpr
        |           2_1_815_pullx.xvg
        |           2_1_949.tpr
        |           2_1_949_pullx.xvg
        |           2_1_957.tpr
        |           2_1_957_pullx.xvg
        |           2_1_96.tpr
        |           2_1_96_pullx.xvg
        |           2_1_970.tpr
        |           2_1_970_pullx.xvg
        |           4_05_1030.tpr
        |           4_05_1030_pullx.xvg
        |           4_05_104.tpr
        |           4_05_104_pullx.xvg
        |           4_05_1052.tpr
        |           4_05_1052_pullx.xvg
        |           4_05_1248.tpr
        |           4_05_1248_pullx.xvg
        |           4_05_1385.tpr
        |           4_05_1385_pullx.xvg
        |           4_05_1428.tpr
        |           4_05_1428_pullx.xvg
        |           4_05_145.tpr
        |           4_05_145_pullx.xvg
        |           4_05_1485.tpr
        |           4_05_1485_pullx.xvg
        |           4_05_1507.tpr
        |           4_05_1507_pullx.xvg
        |           4_05_154.tpr
        |           4_05_154_pullx.xvg
        |           4_05_1605.tpr
        |           4_05_1605_pullx.xvg
        |           4_05_161.tpr
        |           4_05_161_pullx.xvg
        |           4_05_1650.tpr
        |           4_05_1650_pullx.xvg
        |           4_05_1688.tpr
        |           4_05_1688_pullx.xvg
        |           4_05_1705.tpr
        |           4_05_1705_pullx.xvg
        |           4_05_1735.tpr
        |           4_05_1735_pullx.xvg
        |           4_05_1744.tpr
        |           4_05_1744_pullx.xvg
        |           4_05_179.tpr
        |           4_05_179_pullx.xvg
        |           4_05_197.tpr
        |           4_05_197_pullx.xvg
        |           4_05_238.tpr
        |           4_05_238_pullx.xvg
        |           4_05_402.tpr
        |           4_05_402_pullx.xvg
        |           4_05_588.tpr
        |           4_05_588_pullx.xvg
        |           4_05_76.tpr
        |           4_05_76_pullx.xvg
        |           4_05_885.tpr
        |           4_05_885_pullx.xvg
        |           4_05_987.tpr
        |           4_05_987_pullx.xvg
        |           4_1_152.tpr
        |           4_1_152_pullx.xvg
        |           4_1_178.tpr
        |           4_1_178_pullx.xvg
        |           4_1_200.tpr
        |           4_1_200_pullx.xvg
        |           4_1_255.tpr
        |           4_1_255_pullx.xvg
        |           4_1_258.tpr
        |           4_1_258_pullx.xvg
        |           4_1_471.tpr
        |           4_1_471_pullx.xvg
        |           4_1_496.tpr
        |           4_1_496_pullx.xvg
        |           4_1_523.tpr
        |           4_1_523_pullx.xvg
        |           4_1_538.tpr
        |           4_1_538_pullx.xvg
        |           4_1_566.tpr
        |           4_1_566_pullx.xvg
        |           4_1_579.tpr
        |           4_1_579_pullx.xvg
        |           4_1_602.tpr
        |           4_1_602_pullx.xvg
        |           4_1_610.tpr
        |           4_1_610_pullx.xvg
        |           4_1_665.tpr
        |           4_1_665_pullx.xvg
        |           4_1_676.tpr
        |           4_1_676_pullx.xvg
        |           4_1_719.tpr
        |           4_1_719_pullx.xvg
        |           4_1_737.tpr
        |           4_1_737_pullx.xvg
        |           4_1_74.tpr
        |           4_1_74_pullx.xvg
        |           4_1_757.tpr
        |           4_1_757_pullx.xvg
        |           4_1_792.tpr
        |           4_1_792_pullx.xvg
        |           4_1_811.tpr
        |           4_1_811_pullx.xvg
        |           5_05_102.tpr
        |           5_05_102_pullx.xvg
        |           5_05_1117.tpr
        |           5_05_1117_pullx.xvg
        |           5_05_1154.tpr
        |           5_05_1154_pullx.xvg
        |           5_05_1298.tpr
        |           5_05_1298_pullx.xvg
        |           5_05_1389.tpr
        |           5_05_1389_pullx.xvg
        |           5_05_147.tpr
        |           5_05_147_pullx.xvg
        |           5_05_1556.tpr
        |           5_05_1556_pullx.xvg
        |           5_05_1693.tpr
        |           5_05_1693_pullx.xvg
        |           5_05_1878.tpr
        |           5_05_1878_pullx.xvg
        |           5_05_1900.tpr
        |           5_05_1900_pullx.xvg
        |           5_05_2028.tpr
        |           5_05_2028_pullx.xvg
        |           5_05_2037.tpr
        |           5_05_2037_pullx.xvg
        |           5_05_318.tpr
        |           5_05_318_pullx.xvg
        |           5_05_471.tpr
        |           5_05_471_pullx.xvg
        |           5_05_480.tpr
        |           5_05_480_pullx.xvg
        |           5_05_652.tpr
        |           5_05_652_pullx.xvg
        |           5_05_732.tpr
        |           5_05_732_pullx.xvg
        |           5_05_830.tpr
        |           5_05_830_pullx.xvg
        |           5_05_887.tpr
        |           5_05_887_pullx.xvg
        |           5_05_979.tpr
        |           5_05_979_pullx.xvg
        |           5_1_1009.tpr
        |           5_1_1009_pullx.xvg
        |           5_1_1023.tpr
        |           5_1_1023_pullx.xvg
        |           5_1_13.tpr
        |           5_1_13_pullx.xvg
        |           5_1_144.tpr
        |           5_1_144_pullx.xvg
        |           5_1_245.tpr
        |           5_1_245_pullx.xvg
        |           5_1_283.tpr
        |           5_1_283_pullx.xvg
        |           5_1_41.tpr
        |           5_1_41_pullx.xvg
        |           5_1_516.tpr
        |           5_1_516_pullx.xvg
        |           5_1_53.tpr
        |           5_1_53_pullx.xvg
        |           5_1_583.tpr
        |           5_1_583_pullx.xvg
        |           5_1_592.tpr
        |           5_1_592_pullx.xvg
        |           5_1_611.tpr
        |           5_1_611_pullx.xvg
        |           5_1_62.tpr
        |           5_1_62_pullx.xvg
        |           5_1_631.tpr
        |           5_1_631_pullx.xvg
        |           5_1_644.tpr
        |           5_1_644_pullx.xvg
        |           5_1_673.tpr
        |           5_1_673_pullx.xvg
        |           5_1_683.tpr
        |           5_1_683_pullx.xvg
        |           5_1_70.tpr
        |           5_1_70_pullx.xvg
        |           5_1_722.tpr
        |           5_1_722_pullx.xvg
        |           5_1_782.tpr
        |           5_1_782_pullx.xvg
        |           5_1_807.tpr
        |           5_1_807_pullx.xvg
        |           5_1_966.tpr
        |           5_1_966_pullx.xvg
        |           analyze_umbrella_blocks.sh
        |           analyze_umbrella_final.sh
        |           bsProfs_100-120ns.xvg
        |           bsProfs_120-140ns.xvg
        |           bsProfs_140-160ns.xvg
        |           bsProfs_160-180ns.xvg
        |           bsProfs_180-200ns.xvg
        |           bsProfs_20-40ns.xvg
        |           bsProfs_40-60ns.xvg
        |           bsProfs_60-80ns.xvg
        |           bsProfs_80-100ns.xvg
        |           bsProfs_80-200ns.xvg
        |           bsResult_100-120ns.xvg
        |           bsResult_120-140ns.xvg
        |           bsResult_140-160ns.xvg
        |           bsResult_160-180ns.xvg
        |           bsResult_180-200ns.xvg
        |           bsResult_20-40ns.xvg
        |           bsResult_40-60ns.xvg
        |           bsResult_60-80ns.xvg
        |           bsResult_80-100ns.xvg
        |           bsResult_80-200ns.xvg
        |           frames.dat
        |           histo_100-120ns.xvg
        |           histo_120-140ns.xvg
        |           histo_140-160ns.xvg
        |           histo_160-180ns.xvg
        |           histo_180-200ns.xvg
        |           histo_20-40ns.xvg
        |           histo_40-60ns.xvg
        |           histo_60-80ns.xvg
        |           histo_80-100ns.xvg
        |           histo_80-200ns.xvg
        |           profile_100-120ns.xvg
        |           profile_120-140ns.xvg
        |           profile_140-160ns.xvg
        |           profile_160-180ns.xvg
        |           profile_180-200ns.xvg
        |           profile_20-40ns.xvg
        |           profile_40-60ns.xvg
        |           profile_60-80ns.xvg
        |           profile_80-100ns.xvg
        |           profile_80-200ns.xvg
        |           pullx_files.dat
        |           tpr_files.dat
        |           
        +---delta-alphaIb
        |   +---eq
        |   |   |   ATP.gro
        |   |   |   ATP.itp
        |   |   |   GLYM.gro
        |   |   |   GLYM.itp
        |   |   |   ionize.tpr
        |   |   |   md.tpr
        |   |   |   mdout.mdp
        |   |   |   MG.gro
        |   |   |   npt.gro
        |   |   |   npt.mdp
        |   |   |   npt.tpr
        |   |   |   nvt.gro
        |   |   |   nvt.mdp
        |   |   |   nvt.tpr
        |   |   |   posre_ATP.itp
        |   |   |   posre_GLYM.itp
        |   |   |   posre_protein.itp
        |   |   |   production_md.mdp
        |   |   |   protein.gro
        |   |   |   protein.itp
        |   |   |   step6.0_minimization.mdp
        |   |   |   system.gro
        |   |   |   system_box.gro
        |   |   |   system_em.gro
        |   |   |   system_em.tpr
        |   |   |   system_solv.gro
        |   |   |   system_solv_ions.gro
        |   |   |   topol_sys.top
        |   |   |   
        |   |   +---1
        |   |   |       md.tpr
        |   |   |       
        |   |   +---10
        |   |   |       md.tpr
        |   |   |       
        |   |   +---2
        |   |   |       md.tpr
        |   |   |       
        |   |   +---3
        |   |   |       md.tpr
        |   |   |       
        |   |   +---4
        |   |   |       md.tpr
        |   |   |       
        |   |   +---5
        |   |   |       md.tpr
        |   |   |       
        |   |   +---6
        |   |   |       md.tpr
        |   |   |       
        |   |   +---7
        |   |   |       md.tpr
        |   |   |       
        |   |   +---8
        |   |   |       md.tpr
        |   |   |       
        |   |   \---9
        |   |           md.tpr
        |   |           
        |   +---pull
        |   |   |   ATP.itp
        |   |   |   GLYM.itp
        |   |   |   mdout.mdp
        |   |   |   npt.mdp
        |   |   |   nvt.mdp
        |   |   |   posre_ATP.itp
        |   |   |   posre_GLYM.itp
        |   |   |   posre_protein.itp
        |   |   |   protein.itp
        |   |   |   pull_md.mdp
        |   |   |   step6.0_minimization.mdp
        |   |   |   topol.top
        |   |   |   
        |   |   +---1
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---2
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---3
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---4
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---5
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---6
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   +---7
        |   |   |       eq_md.gro
        |   |   |       npt.tpr
        |   |   |       nvt.tpr
        |   |   |       pull_em.tpr
        |   |   |       pull_md_0.05ms.tpr
        |   |   |       pull_md_0.1ms.tpr
        |   |   |       
        |   |   \---8
        |   |           eq_md.gro
        |   |           npt.tpr
        |   |           nvt.tpr
        |   |           pull_em.tpr
        |   |           pull_md_0.05ms.tpr
        |   |           pull_md_0.1ms.tpr
        |   |           
        |   \---umbrella
        |           1_05_100.tpr
        |           1_05_100_pullx.xvg
        |           1_05_115.tpr
        |           1_05_1156.tpr
        |           1_05_1156_pullx.xvg
        |           1_05_115_pullx.xvg
        |           1_05_1169.tpr
        |           1_05_1169_pullx.xvg
        |           1_05_1237.tpr
        |           1_05_1237_pullx.xvg
        |           1_05_1266.tpr
        |           1_05_1266_pullx.xvg
        |           1_05_1368.tpr
        |           1_05_1368_pullx.xvg
        |           1_05_200.tpr
        |           1_05_200_pullx.xvg
        |           1_05_269.tpr
        |           1_05_269_pullx.xvg
        |           1_05_36.tpr
        |           1_05_36_pullx.xvg
        |           1_05_392.tpr
        |           1_05_392_pullx.xvg
        |           1_05_416.tpr
        |           1_05_416_pullx.xvg
        |           1_05_51.tpr
        |           1_05_51_pullx.xvg
        |           1_05_609.tpr
        |           1_05_609_pullx.xvg
        |           1_05_7.tpr
        |           1_05_728.tpr
        |           1_05_728_pullx.xvg
        |           1_05_786.tpr
        |           1_05_786_pullx.xvg
        |           1_05_7_pullx.xvg
        |           1_05_854.tpr
        |           1_05_854_pullx.xvg
        |           1_05_878.tpr
        |           1_05_878_pullx.xvg
        |           1_05_905.tpr
        |           1_05_905_pullx.xvg
        |           1_05_928.tpr
        |           1_05_928_pullx.xvg
        |           1_05_957.tpr
        |           1_05_957_pullx.xvg
        |           1_1_121.tpr
        |           1_1_121_pullx.xvg
        |           1_1_15.tpr
        |           1_1_15_pullx.xvg
        |           1_1_177.tpr
        |           1_1_177_pullx.xvg
        |           1_1_183.tpr
        |           1_1_183_pullx.xvg
        |           1_1_200.tpr
        |           1_1_200_pullx.xvg
        |           1_1_21.tpr
        |           1_1_21_pullx.xvg
        |           1_1_239.tpr
        |           1_1_239_pullx.xvg
        |           1_1_308.tpr
        |           1_1_308_pullx.xvg
        |           1_1_359.tpr
        |           1_1_359_pullx.xvg
        |           1_1_406.tpr
        |           1_1_406_pullx.xvg
        |           1_1_427.tpr
        |           1_1_427_pullx.xvg
        |           1_1_44.tpr
        |           1_1_446.tpr
        |           1_1_446_pullx.xvg
        |           1_1_44_pullx.xvg
        |           1_1_46.tpr
        |           1_1_463.tpr
        |           1_1_463_pullx.xvg
        |           1_1_46_pullx.xvg
        |           1_1_479.tpr
        |           1_1_479_pullx.xvg
        |           1_1_503.tpr
        |           1_1_503_pullx.xvg
        |           1_1_509.tpr
        |           1_1_509_pullx.xvg
        |           1_1_53.tpr
        |           1_1_53_pullx.xvg
        |           1_1_590.tpr
        |           1_1_590_pullx.xvg
        |           1_1_632.tpr
        |           1_1_632_pullx.xvg
        |           1_1_677.tpr
        |           1_1_677_pullx.xvg
        |           1_1_7.tpr
        |           1_1_7_pullx.xvg
        |           2_05_1074.tpr
        |           2_05_1074_pullx.xvg
        |           2_05_108.tpr
        |           2_05_108_pullx.xvg
        |           2_05_1101.tpr
        |           2_05_1101_pullx.xvg
        |           2_05_1155.tpr
        |           2_05_1155_pullx.xvg
        |           2_05_1164.tpr
        |           2_05_1164_pullx.xvg
        |           2_05_1197.tpr
        |           2_05_1197_pullx.xvg
        |           2_05_1224.tpr
        |           2_05_1224_pullx.xvg
        |           2_05_1260.tpr
        |           2_05_1260_pullx.xvg
        |           2_05_1287.tpr
        |           2_05_1287_pullx.xvg
        |           2_05_1302.tpr
        |           2_05_1302_pullx.xvg
        |           2_05_1404.tpr
        |           2_05_1404_pullx.xvg
        |           2_05_1459.tpr
        |           2_05_1459_pullx.xvg
        |           2_05_1490.tpr
        |           2_05_1490_pullx.xvg
        |           2_05_153.tpr
        |           2_05_153_pullx.xvg
        |           2_05_1588.tpr
        |           2_05_1588_pullx.xvg
        |           2_05_2.tpr
        |           2_05_204.tpr
        |           2_05_204_pullx.xvg
        |           2_05_255.tpr
        |           2_05_255_pullx.xvg
        |           2_05_26.tpr
        |           2_05_26_pullx.xvg
        |           2_05_2_pullx.xvg
        |           2_05_306.tpr
        |           2_05_306_pullx.xvg
        |           2_05_339.tpr
        |           2_05_339_pullx.xvg
        |           2_05_387.tpr
        |           2_05_387_pullx.xvg
        |           2_05_464.tpr
        |           2_05_464_pullx.xvg
        |           2_05_646.tpr
        |           2_05_646_pullx.xvg
        |           2_05_720.tpr
        |           2_05_720_pullx.xvg
        |           2_05_80.tpr
        |           2_05_80_pullx.xvg
        |           2_05_830.tpr
        |           2_05_830_pullx.xvg
        |           2_05_902.tpr
        |           2_05_902_pullx.xvg
        |           2_1_1.tpr
        |           2_1_167.tpr
        |           2_1_167_pullx.xvg
        |           2_1_189.tpr
        |           2_1_189_pullx.xvg
        |           2_1_1_pullx.xvg
        |           2_1_219.tpr
        |           2_1_219_pullx.xvg
        |           2_1_23.tpr
        |           2_1_23_pullx.xvg
        |           2_1_263.tpr
        |           2_1_263_pullx.xvg
        |           2_1_298.tpr
        |           2_1_298_pullx.xvg
        |           2_1_305.tpr
        |           2_1_305_pullx.xvg
        |           2_1_310.tpr
        |           2_1_310_pullx.xvg
        |           2_1_368.tpr
        |           2_1_368_pullx.xvg
        |           2_1_427.tpr
        |           2_1_427_pullx.xvg
        |           2_1_478.tpr
        |           2_1_478_pullx.xvg
        |           2_1_51.tpr
        |           2_1_51_pullx.xvg
        |           2_1_522.tpr
        |           2_1_522_pullx.xvg
        |           2_1_576.tpr
        |           2_1_576_pullx.xvg
        |           2_1_623.tpr
        |           2_1_623_pullx.xvg
        |           2_1_631.tpr
        |           2_1_631_pullx.xvg
        |           2_1_648.tpr
        |           2_1_648_pullx.xvg
        |           2_1_658.tpr
        |           2_1_658_pullx.xvg
        |           2_1_666.tpr
        |           2_1_666_pullx.xvg
        |           2_1_672.tpr
        |           2_1_672_pullx.xvg
        |           2_1_696.tpr
        |           2_1_696_pullx.xvg
        |           2_1_707.tpr
        |           2_1_707_pullx.xvg
        |           2_1_763.tpr
        |           2_1_763_pullx.xvg
        |           2_1_78.tpr
        |           2_1_78_pullx.xvg
        |           2_1_832.tpr
        |           2_1_832_pullx.xvg
        |           2_1_842.tpr
        |           2_1_842_pullx.xvg
        |           2_1_85.tpr
        |           2_1_85_pullx.xvg
        |           4_05_112.tpr
        |           4_05_112_pullx.xvg
        |           4_05_1133.tpr
        |           4_05_1133_pullx.xvg
        |           4_05_1249.tpr
        |           4_05_1249_pullx.xvg
        |           4_05_1345.tpr
        |           4_05_1345_pullx.xvg
        |           4_05_1384.tpr
        |           4_05_1384_pullx.xvg
        |           4_05_1408.tpr
        |           4_05_1408_pullx.xvg
        |           4_05_1423.tpr
        |           4_05_1423_pullx.xvg
        |           4_05_1454.tpr
        |           4_05_1454_pullx.xvg
        |           4_05_1492.tpr
        |           4_05_1492_pullx.xvg
        |           4_05_155.tpr
        |           4_05_155_pullx.xvg
        |           4_05_1576.tpr
        |           4_05_1576_pullx.xvg
        |           4_05_1651.tpr
        |           4_05_1651_pullx.xvg
        |           4_05_1769.tpr
        |           4_05_1769_pullx.xvg
        |           4_05_193.tpr
        |           4_05_193_pullx.xvg
        |           4_05_206.tpr
        |           4_05_206_pullx.xvg
        |           4_05_258.tpr
        |           4_05_258_pullx.xvg
        |           4_05_315.tpr
        |           4_05_315_pullx.xvg
        |           4_05_339.tpr
        |           4_05_339_pullx.xvg
        |           4_05_350.tpr
        |           4_05_350_pullx.xvg
        |           4_05_464.tpr
        |           4_05_464_pullx.xvg
        |           4_05_60.tpr
        |           4_05_60_pullx.xvg
        |           4_05_639.tpr
        |           4_05_639_pullx.xvg
        |           4_05_708.tpr
        |           4_05_708_pullx.xvg
        |           4_05_824.tpr
        |           4_05_824_pullx.xvg
        |           4_05_845.tpr
        |           4_05_845_pullx.xvg
        |           4_05_990.tpr
        |           4_05_990_pullx.xvg
        |           4_1_13.tpr
        |           4_1_139.tpr
        |           4_1_139_pullx.xvg
        |           4_1_13_pullx.xvg
        |           4_1_151.tpr
        |           4_1_151_pullx.xvg
        |           4_1_183.tpr
        |           4_1_183_pullx.xvg
        |           4_1_185.tpr
        |           4_1_185_pullx.xvg
        |           4_1_231.tpr
        |           4_1_231_pullx.xvg
        |           4_1_253.tpr
        |           4_1_253_pullx.xvg
        |           4_1_296.tpr
        |           4_1_296_pullx.xvg
        |           4_1_34.tpr
        |           4_1_344.tpr
        |           4_1_344_pullx.xvg
        |           4_1_34_pullx.xvg
        |           4_1_403.tpr
        |           4_1_403_pullx.xvg
        |           4_1_409.tpr
        |           4_1_409_pullx.xvg
        |           4_1_42.tpr
        |           4_1_42_pullx.xvg
        |           4_1_481.tpr
        |           4_1_481_pullx.xvg
        |           4_1_490.tpr
        |           4_1_490_pullx.xvg
        |           4_1_495.tpr
        |           4_1_495_pullx.xvg
        |           4_1_528.tpr
        |           4_1_528_pullx.xvg
        |           4_1_544.tpr
        |           4_1_544_pullx.xvg
        |           4_1_64.tpr
        |           4_1_64_pullx.xvg
        |           4_1_656.tpr
        |           4_1_656_pullx.xvg
        |           4_1_67.tpr
        |           4_1_675.tpr
        |           4_1_675_pullx.xvg
        |           4_1_67_pullx.xvg
        |           4_1_684.tpr
        |           4_1_684_pullx.xvg
        |           4_1_7.tpr
        |           4_1_710.tpr
        |           4_1_710_pullx.xvg
        |           4_1_727.tpr
        |           4_1_727_pullx.xvg
        |           4_1_765.tpr
        |           4_1_765_pullx.xvg
        |           4_1_793.tpr
        |           4_1_793_pullx.xvg
        |           4_1_7_pullx.xvg
        |           4_1_830.tpr
        |           4_1_830_pullx.xvg
        |           4_1_872.tpr
        |           4_1_872_pullx.xvg
        |           5_05_1039.tpr
        |           5_05_1039_pullx.xvg
        |           5_05_1111.tpr
        |           5_05_1111_pullx.xvg
        |           5_05_1238.tpr
        |           5_05_1238_pullx.xvg
        |           5_05_1383.tpr
        |           5_05_1383_pullx.xvg
        |           5_05_14.tpr
        |           5_05_1468.tpr
        |           5_05_1468_pullx.xvg
        |           5_05_14_pullx.xvg
        |           5_05_1529.tpr
        |           5_05_1529_pullx.xvg
        |           5_05_163.tpr
        |           5_05_163_pullx.xvg
        |           5_05_1700.tpr
        |           5_05_1700_pullx.xvg
        |           5_05_1744.tpr
        |           5_05_1744_pullx.xvg
        |           5_05_1793.tpr
        |           5_05_1793_pullx.xvg
        |           5_05_180.tpr
        |           5_05_180_pullx.xvg
        |           5_05_1857.tpr
        |           5_05_1857_pullx.xvg
        |           5_05_1906.tpr
        |           5_05_1906_pullx.xvg
        |           5_05_2021.tpr
        |           5_05_2021_pullx.xvg
        |           5_05_2105.tpr
        |           5_05_2105_pullx.xvg
        |           5_05_2199.tpr
        |           5_05_2199_pullx.xvg
        |           5_05_2211.tpr
        |           5_05_2211_pullx.xvg
        |           5_05_2246.tpr
        |           5_05_2246_pullx.xvg
        |           5_05_2285.tpr
        |           5_05_2285_pullx.xvg
        |           5_05_2327.tpr
        |           5_05_2327_pullx.xvg
        |           5_05_240.tpr
        |           5_05_240_pullx.xvg
        |           5_05_2467.tpr
        |           5_05_2467_pullx.xvg
        |           5_05_2499.tpr
        |           5_05_2499_pullx.xvg
        |           5_05_33.tpr
        |           5_05_33_pullx.xvg
        |           5_05_349.tpr
        |           5_05_349_pullx.xvg
        |           5_05_391.tpr
        |           5_05_391_pullx.xvg
        |           5_05_404.tpr
        |           5_05_404_pullx.xvg
        |           5_05_421.tpr
        |           5_05_421_pullx.xvg
        |           5_05_513.tpr
        |           5_05_513_pullx.xvg
        |           5_05_556.tpr
        |           5_05_556_pullx.xvg
        |           5_05_72.tpr
        |           5_05_72_pullx.xvg
        |           5_05_763.tpr
        |           5_05_763_pullx.xvg
        |           5_05_824.tpr
        |           5_05_824_pullx.xvg
        |           5_05_976.tpr
        |           5_05_976_pullx.xvg
        |           5_1_0.tpr
        |           5_1_0_pullx.xvg
        |           5_1_1024.tpr
        |           5_1_1024_pullx.xvg
        |           5_1_1038.tpr
        |           5_1_1038_pullx.xvg
        |           5_1_1061.tpr
        |           5_1_1061_pullx.xvg
        |           5_1_1087.tpr
        |           5_1_1087_pullx.xvg
        |           5_1_1161.tpr
        |           5_1_1161_pullx.xvg
        |           5_1_117.tpr
        |           5_1_117_pullx.xvg
        |           5_1_122.tpr
        |           5_1_122_pullx.xvg
        |           5_1_143.tpr
        |           5_1_143_pullx.xvg
        |           5_1_173.tpr
        |           5_1_173_pullx.xvg
        |           5_1_19.tpr
        |           5_1_19_pullx.xvg
        |           5_1_207.tpr
        |           5_1_207_pullx.xvg
        |           5_1_241.tpr
        |           5_1_241_pullx.xvg
        |           5_1_305.tpr
        |           5_1_305_pullx.xvg
        |           5_1_355.tpr
        |           5_1_355_pullx.xvg
        |           5_1_431.tpr
        |           5_1_431_pullx.xvg
        |           5_1_456.tpr
        |           5_1_456_pullx.xvg
        |           5_1_50.tpr
        |           5_1_50_pullx.xvg
        |           5_1_511.tpr
        |           5_1_511_pullx.xvg
        |           5_1_55.tpr
        |           5_1_556.tpr
        |           5_1_556_pullx.xvg
        |           5_1_55_pullx.xvg
        |           5_1_615.tpr
        |           5_1_615_pullx.xvg
        |           5_1_659.tpr
        |           5_1_659_pullx.xvg
        |           5_1_70.tpr
        |           5_1_70_pullx.xvg
        |           5_1_751.tpr
        |           5_1_751_pullx.xvg
        |           5_1_803.tpr
        |           5_1_803_pullx.xvg
        |           5_1_827.tpr
        |           5_1_827_pullx.xvg
        |           5_1_877.tpr
        |           5_1_877_pullx.xvg
        |           5_1_881.tpr
        |           5_1_881_pullx.xvg
        |           5_1_938.tpr
        |           5_1_938_pullx.xvg
        |           5_1_952.tpr
        |           5_1_952_pullx.xvg
        |           5_1_959.tpr
        |           5_1_959_pullx.xvg
        |           5_1_990.tpr
        |           5_1_990_pullx.xvg
        |           6_05_1124.tpr
        |           6_05_1124_pullx.xvg
        |           6_05_1248.tpr
        |           6_05_1248_pullx.xvg
        |           6_05_1383.tpr
        |           6_05_1383_pullx.xvg
        |           6_05_1451.tpr
        |           6_05_1451_pullx.xvg
        |           6_05_1505.tpr
        |           6_05_1505_pullx.xvg
        |           6_05_1535.tpr
        |           6_05_1535_pullx.xvg
        |           6_05_1573.tpr
        |           6_05_1573_pullx.xvg
        |           6_05_1576.tpr
        |           6_05_1576_pullx.xvg
        |           6_05_1594.tpr
        |           6_05_1594_pullx.xvg
        |           6_05_1626.tpr
        |           6_05_1626_pullx.xvg
        |           6_05_1640.tpr
        |           6_05_1640_pullx.xvg
        |           6_05_1731.tpr
        |           6_05_1731_pullx.xvg
        |           6_05_1742.tpr
        |           6_05_1742_pullx.xvg
        |           6_05_1801.tpr
        |           6_05_1801_pullx.xvg
        |           6_05_1838.tpr
        |           6_05_1838_pullx.xvg
        |           6_05_2021.tpr
        |           6_05_2021_pullx.xvg
        |           6_05_204.tpr
        |           6_05_204_pullx.xvg
        |           6_05_2098.tpr
        |           6_05_2098_pullx.xvg
        |           6_05_2173.tpr
        |           6_05_2173_pullx.xvg
        |           6_05_221.tpr
        |           6_05_221_pullx.xvg
        |           6_05_278.tpr
        |           6_05_278_pullx.xvg
        |           6_05_305.tpr
        |           6_05_305_pullx.xvg
        |           6_05_32.tpr
        |           6_05_32_pullx.xvg
        |           6_05_4.tpr
        |           6_05_410.tpr
        |           6_05_410_pullx.xvg
        |           6_05_437.tpr
        |           6_05_437_pullx.xvg
        |           6_05_480.tpr
        |           6_05_480_pullx.xvg
        |           6_05_4_pullx.xvg
        |           6_05_543.tpr
        |           6_05_543_pullx.xvg
        |           6_05_58.tpr
        |           6_05_58_pullx.xvg
        |           6_05_668.tpr
        |           6_05_668_pullx.xvg
        |           6_05_738.tpr
        |           6_05_738_pullx.xvg
        |           6_05_873.tpr
        |           6_05_873_pullx.xvg
        |           6_05_978.tpr
        |           6_05_978_pullx.xvg
        |           6_05_99.tpr
        |           6_05_99_pullx.xvg
        |           6_1_1029.tpr
        |           6_1_1029_pullx.xvg
        |           6_1_136.tpr
        |           6_1_136_pullx.xvg
        |           6_1_140.tpr
        |           6_1_140_pullx.xvg
        |           6_1_148.tpr
        |           6_1_148_pullx.xvg
        |           6_1_171.tpr
        |           6_1_171_pullx.xvg
        |           6_1_22.tpr
        |           6_1_224.tpr
        |           6_1_224_pullx.xvg
        |           6_1_22_pullx.xvg
        |           6_1_233.tpr
        |           6_1_233_pullx.xvg
        |           6_1_29.tpr
        |           6_1_291.tpr
        |           6_1_291_pullx.xvg
        |           6_1_29_pullx.xvg
        |           6_1_322.tpr
        |           6_1_322_pullx.xvg
        |           6_1_404.tpr
        |           6_1_404_pullx.xvg
        |           6_1_447.tpr
        |           6_1_447_pullx.xvg
        |           6_1_482.tpr
        |           6_1_482_pullx.xvg
        |           6_1_543.tpr
        |           6_1_543_pullx.xvg
        |           6_1_62.tpr
        |           6_1_62_pullx.xvg
        |           6_1_647.tpr
        |           6_1_647_pullx.xvg
        |           6_1_654.tpr
        |           6_1_654_pullx.xvg
        |           6_1_711.tpr
        |           6_1_711_pullx.xvg
        |           6_1_73.tpr
        |           6_1_73_pullx.xvg
        |           6_1_762.tpr
        |           6_1_762_pullx.xvg
        |           6_1_8.tpr
        |           6_1_801.tpr
        |           6_1_801_pullx.xvg
        |           6_1_821.tpr
        |           6_1_821_pullx.xvg
        |           6_1_844.tpr
        |           6_1_844_pullx.xvg
        |           6_1_872.tpr
        |           6_1_872_pullx.xvg
        |           6_1_895.tpr
        |           6_1_895_pullx.xvg
        |           6_1_8_pullx.xvg
        |           6_1_919.tpr
        |           6_1_919_pullx.xvg
        |           6_1_962.tpr
        |           6_1_962_pullx.xvg
        |           6_1_983.tpr
        |           6_1_983_pullx.xvg
        |           8_05_106.tpr
        |           8_05_106_pullx.xvg
        |           8_05_1080.tpr
        |           8_05_1080_pullx.xvg
        |           8_05_1183.tpr
        |           8_05_1183_pullx.xvg
        |           8_05_16.tpr
        |           8_05_1656.tpr
        |           8_05_1656_pullx.xvg
        |           8_05_16_pullx.xvg
        |           8_05_1776.tpr
        |           8_05_1776_pullx.xvg
        |           8_05_192.tpr
        |           8_05_192_pullx.xvg
        |           8_05_1936.tpr
        |           8_05_1936_pullx.xvg
        |           8_05_1976.tpr
        |           8_05_1976_pullx.xvg
        |           8_05_2113.tpr
        |           8_05_2113_pullx.xvg
        |           8_05_2206.tpr
        |           8_05_2206_pullx.xvg
        |           8_05_2248.tpr
        |           8_05_2248_pullx.xvg
        |           8_05_2327.tpr
        |           8_05_2327_pullx.xvg
        |           8_05_2403.tpr
        |           8_05_2403_pullx.xvg
        |           8_05_2455.tpr
        |           8_05_2455_pullx.xvg
        |           8_05_2574.tpr
        |           8_05_2574_pullx.xvg
        |           8_05_2625.tpr
        |           8_05_2625_pullx.xvg
        |           8_05_2649.tpr
        |           8_05_2649_pullx.xvg
        |           8_05_266.tpr
        |           8_05_266_pullx.xvg
        |           8_05_296.tpr
        |           8_05_296_pullx.xvg
        |           8_05_30.tpr
        |           8_05_30_pullx.xvg
        |           8_05_351.tpr
        |           8_05_351_pullx.xvg
        |           8_05_374.tpr
        |           8_05_374_pullx.xvg
        |           8_05_403.tpr
        |           8_05_403_pullx.xvg
        |           8_05_519.tpr
        |           8_05_519_pullx.xvg
        |           8_05_543.tpr
        |           8_05_543_pullx.xvg
        |           8_05_657.tpr
        |           8_05_657_pullx.xvg
        |           8_05_76.tpr
        |           8_05_76_pullx.xvg
        |           8_05_814.tpr
        |           8_05_814_pullx.xvg
        |           8_1_1.tpr
        |           8_1_1019.tpr
        |           8_1_1019_pullx.xvg
        |           8_1_1080.tpr
        |           8_1_1080_pullx.xvg
        |           8_1_11.tpr
        |           8_1_1139.tpr
        |           8_1_1139_pullx.xvg
        |           8_1_1161.tpr
        |           8_1_1161_pullx.xvg
        |           8_1_1166.tpr
        |           8_1_1166_pullx.xvg
        |           8_1_1194.tpr
        |           8_1_1194_pullx.xvg
        |           8_1_11_pullx.xvg
        |           8_1_1201.tpr
        |           8_1_1201_pullx.xvg
        |           8_1_1228.tpr
        |           8_1_1228_pullx.xvg
        |           8_1_1241.tpr
        |           8_1_1241_pullx.xvg
        |           8_1_1276.tpr
        |           8_1_1276_pullx.xvg
        |           8_1_1307.tpr
        |           8_1_1307_pullx.xvg
        |           8_1_1437.tpr
        |           8_1_1437_pullx.xvg
        |           8_1_148.tpr
        |           8_1_148_pullx.xvg
        |           8_1_195.tpr
        |           8_1_195_pullx.xvg
        |           8_1_1_pullx.xvg
        |           8_1_21.tpr
        |           8_1_21_pullx.xvg
        |           8_1_231.tpr
        |           8_1_231_pullx.xvg
        |           8_1_271.tpr
        |           8_1_271_pullx.xvg
        |           8_1_299.tpr
        |           8_1_299_pullx.xvg
        |           8_1_315.tpr
        |           8_1_315_pullx.xvg
        |           8_1_353.tpr
        |           8_1_353_pullx.xvg
        |           8_1_387.tpr
        |           8_1_387_pullx.xvg
        |           8_1_498.tpr
        |           8_1_498_pullx.xvg
        |           8_1_550.tpr
        |           8_1_550_pullx.xvg
        |           8_1_634.tpr
        |           8_1_634_pullx.xvg
        |           8_1_649.tpr
        |           8_1_649_pullx.xvg
        |           8_1_773.tpr
        |           8_1_773_pullx.xvg
        |           8_1_80.tpr
        |           8_1_80_pullx.xvg
        |           8_1_818.tpr
        |           8_1_818_pullx.xvg
        |           analyze_umbrella_blocks.sh
        |           analyze_umbrella_final.sh
        |           bsProfs_100-120ns.xvg
        |           bsProfs_120-140ns.xvg
        |           bsProfs_140-160ns.xvg
        |           bsProfs_160-180ns.xvg
        |           bsProfs_180-200ns.xvg
        |           bsProfs_20-40ns.xvg
        |           bsProfs_40-60ns.xvg
        |           bsProfs_60-80ns.xvg
        |           bsProfs_80-100ns.xvg
        |           bsProfs_80-200ns.xvg
        |           bsResult_100-120ns.xvg
        |           bsResult_120-140ns.xvg
        |           bsResult_140-160ns.xvg
        |           bsResult_160-180ns.xvg
        |           bsResult_180-200ns.xvg
        |           bsResult_20-40ns.xvg
        |           bsResult_40-60ns.xvg
        |           bsResult_60-80ns.xvg
        |           bsResult_80-100ns.xvg
        |           bsResult_80-200ns.xvg
        |           frames.dat
        |           histo_100-120ns.xvg
        |           histo_120-140ns.xvg
        |           histo_140-160ns.xvg
        |           histo_160-180ns.xvg
        |           histo_180-200ns.xvg
        |           histo_20-40ns.xvg
        |           histo_40-60ns.xvg
        |           histo_60-80ns.xvg
        |           histo_80-100ns.xvg
        |           histo_80-200ns.xvg
        |           profile_100-120ns.xvg
        |           profile_120-140ns.xvg
        |           profile_140-160ns.xvg
        |           profile_160-180ns.xvg
        |           profile_180-200ns.xvg
        |           profile_20-40ns.xvg
        |           profile_40-60ns.xvg
        |           profile_60-80ns.xvg
        |           profile_80-100ns.xvg
        |           profile_80-200ns.xvg
        |           pullx_files.dat
        |           tpr_files.dat
        |           
        \---membrane
            +---eq
            |   |   GLYM.itp
            |   |   md_eq.mdp
            |   |   npt1.mdp
            |   |   npt1.tpr
            |   |   npt2.mdp
            |   |   npt2.tpr
            |   |   nvt.mdp
            |   |   nvt.tpr
            |   |   POPC.itp
            |   |   posre_GLYM.itp
            |   |   posre_POPC.itp
            |   |   system_em.gro
            |   |   topol.top
            |   |   
            |   +---1
            |   |       md_eq.tpr
            |   |       
            |   +---2
            |   |       md_eq.tpr
            |   |       
            |   \---3
            |           md_eq.tpr
            |           
            +---pull
            |   |   GLYM.itp
            |   |   ndx_groups_pull
            |   |   npt.mdp
            |   |   nvt.mdp
            |   |   POPC.itp
            |   |   posre_GLYM.itp
            |   |   posre_POPC.itp
            |   |   pull_md.mdp
            |   |   pull_setup.sh
            |   |   step6.0_minimization.mdp
            |   |   topol.top
            |   |   
            |   +---1
            |   |       last_frame_mol.gro
            |   |       npt.tpr
            |   |       nvt.tpr
            |   |       pull_em.tpr
            |   |       pull_md_0.05ms.tpr
            |   |       pull_md_0.1ms.tpr
            |   |       
            |   +---2
            |   |       last_frame_mol.gro
            |   |       npt.tpr
            |   |       nvt.tpr
            |   |       pull_em.tpr
            |   |       pull_md_0.05ms.tpr
            |   |       pull_md_0.1ms.tpr
            |   |       
            |   \---3
            |           last_frame_mol.gro
            |           npt.tpr
            |           nvt.tpr
            |           pull_em.tpr
            |           pull_md_0.05ms.tpr
            |           pull_md_0.1ms.tpr
            |           
            \---umbrella
                    1_05_1009.tpr
                    1_05_1009_pullx.xvg
                    1_05_1054.tpr
                    1_05_1054_pullx.xvg
                    1_05_115.tpr
                    1_05_115_pullx.xvg
                    1_05_1187.tpr
                    1_05_1187_pullx.xvg
                    1_05_1234.tpr
                    1_05_1234_pullx.xvg
                    1_05_189.tpr
                    1_05_189_pullx.xvg
                    1_05_196.tpr
                    1_05_196_pullx.xvg
                    1_05_223.tpr
                    1_05_223_pullx.xvg
                    1_05_25.tpr
                    1_05_25_pullx.xvg
                    1_05_304.tpr
                    1_05_304_pullx.xvg
                    1_05_43.tpr
                    1_05_43_pullx.xvg
                    1_05_565.tpr
                    1_05_565_pullx.xvg
                    1_05_59.tpr
                    1_05_59_pullx.xvg
                    1_05_675.tpr
                    1_05_675_pullx.xvg
                    1_05_714.tpr
                    1_05_714_pullx.xvg
                    1_05_73.tpr
                    1_05_73_pullx.xvg
                    1_05_77.tpr
                    1_05_77_pullx.xvg
                    1_05_822.tpr
                    1_05_822_pullx.xvg
                    1_05_83.tpr
                    1_05_83_pullx.xvg
                    1_05_906.tpr
                    1_05_906_pullx.xvg
                    1_05_96.tpr
                    1_05_96_pullx.xvg
                    1_1_0.tpr
                    1_1_0_pullx.xvg
                    1_1_152.tpr
                    1_1_152_pullx.xvg
                    1_1_159.tpr
                    1_1_159_pullx.xvg
                    1_1_213.tpr
                    1_1_213_pullx.xvg
                    1_1_220.tpr
                    1_1_220_pullx.xvg
                    1_1_301.tpr
                    1_1_301_pullx.xvg
                    1_1_374.tpr
                    1_1_374_pullx.xvg
                    1_1_397.tpr
                    1_1_397_pullx.xvg
                    1_1_408.tpr
                    1_1_408_pullx.xvg
                    1_1_433.tpr
                    1_1_433_pullx.xvg
                    1_1_552.tpr
                    1_1_552_pullx.xvg
                    1_1_563.tpr
                    1_1_563_pullx.xvg
                    1_1_611.tpr
                    1_1_611_pullx.xvg
                    1_1_698.tpr
                    1_1_698_pullx.xvg
                    1_1_748.tpr
                    1_1_748_pullx.xvg
                    1_1_78.tpr
                    1_1_783.tpr
                    1_1_783_pullx.xvg
                    1_1_78_pullx.xvg
                    1_1_865.tpr
                    1_1_865_pullx.xvg
                    1_1_88.tpr
                    1_1_88_pullx.xvg
                    1_1_924.tpr
                    1_1_924_pullx.xvg
                    1_1_991.tpr
                    1_1_991_pullx.xvg
                    2_05_1051.tpr
                    2_05_1051_pullx.xvg
                    2_05_1132.tpr
                    2_05_1132_pullx.xvg
                    2_05_12.tpr
                    2_05_1273.tpr
                    2_05_1273_pullx.xvg
                    2_05_12_pullx.xvg
                    2_05_134.tpr
                    2_05_134_pullx.xvg
                    2_05_139.tpr
                    2_05_1391.tpr
                    2_05_1391_pullx.xvg
                    2_05_139_pullx.xvg
                    2_05_143.tpr
                    2_05_143_pullx.xvg
                    2_05_1526.tpr
                    2_05_1526_pullx.xvg
                    2_05_1649.tpr
                    2_05_1649_pullx.xvg
                    2_05_170.tpr
                    2_05_170_pullx.xvg
                    2_05_180.tpr
                    2_05_180_pullx.xvg
                    2_05_184.tpr
                    2_05_184_pullx.xvg
                    2_05_190.tpr
                    2_05_190_pullx.xvg
                    2_05_259.tpr
                    2_05_259_pullx.xvg
                    2_05_3.tpr
                    2_05_30.tpr
                    2_05_30_pullx.xvg
                    2_05_38.tpr
                    2_05_38_pullx.xvg
                    2_05_392.tpr
                    2_05_392_pullx.xvg
                    2_05_3_pullx.xvg
                    2_05_433.tpr
                    2_05_433_pullx.xvg
                    2_05_472.tpr
                    2_05_472_pullx.xvg
                    2_05_513.tpr
                    2_05_513_pullx.xvg
                    2_05_58.tpr
                    2_05_58_pullx.xvg
                    2_05_650.tpr
                    2_05_650_pullx.xvg
                    2_05_66.tpr
                    2_05_66_pullx.xvg
                    2_05_842.tpr
                    2_05_842_pullx.xvg
                    2_1_172.tpr
                    2_1_172_pullx.xvg
                    2_1_185.tpr
                    2_1_185_pullx.xvg
                    2_1_196.tpr
                    2_1_196_pullx.xvg
                    2_1_2.tpr
                    2_1_202.tpr
                    2_1_202_pullx.xvg
                    2_1_217.tpr
                    2_1_217_pullx.xvg
                    2_1_231.tpr
                    2_1_231_pullx.xvg
                    2_1_238.tpr
                    2_1_238_pullx.xvg
                    2_1_256.tpr
                    2_1_256_pullx.xvg
                    2_1_265.tpr
                    2_1_265_pullx.xvg
                    2_1_266.tpr
                    2_1_266_pullx.xvg
                    2_1_267.tpr
                    2_1_267_pullx.xvg
                    2_1_2_pullx.xvg
                    2_1_41.tpr
                    2_1_41_pullx.xvg
                    2_1_428.tpr
                    2_1_428_pullx.xvg
                    2_1_454.tpr
                    2_1_454_pullx.xvg
                    2_1_476.tpr
                    2_1_476_pullx.xvg
                    2_1_51.tpr
                    2_1_51_pullx.xvg
                    2_1_529.tpr
                    2_1_529_pullx.xvg
                    2_1_54.tpr
                    2_1_54_pullx.xvg
                    2_1_614.tpr
                    2_1_614_pullx.xvg
                    2_1_642.tpr
                    2_1_642_pullx.xvg
                    2_1_65.tpr
                    2_1_65_pullx.xvg
                    2_1_720.tpr
                    2_1_720_pullx.xvg
                    2_1_772.tpr
                    2_1_772_pullx.xvg
                    2_1_797.tpr
                    2_1_797_pullx.xvg
                    2_1_859.tpr
                    2_1_859_pullx.xvg
                    2_1_91.tpr
                    2_1_91_pullx.xvg
                    2_1_935.tpr
                    2_1_935_pullx.xvg
                    3_05_1009.tpr
                    3_05_1009_pullx.xvg
                    3_05_112.tpr
                    3_05_1128.tpr
                    3_05_1128_pullx.xvg
                    3_05_112_pullx.xvg
                    3_05_1194.tpr
                    3_05_1194_pullx.xvg
                    3_05_1196.tpr
                    3_05_1196_pullx.xvg
                    3_05_1374.tpr
                    3_05_1374_pullx.xvg
                    3_05_1448.tpr
                    3_05_1448_pullx.xvg
                    3_05_146.tpr
                    3_05_146_pullx.xvg
                    3_05_1512.tpr
                    3_05_1512_pullx.xvg
                    3_05_1603.tpr
                    3_05_1603_pullx.xvg
                    3_05_163.tpr
                    3_05_163_pullx.xvg
                    3_05_1756.tpr
                    3_05_1756_pullx.xvg
                    3_05_1788.tpr
                    3_05_1788_pullx.xvg
                    3_05_180.tpr
                    3_05_180_pullx.xvg
                    3_05_266.tpr
                    3_05_266_pullx.xvg
                    3_05_293.tpr
                    3_05_293_pullx.xvg
                    3_05_317.tpr
                    3_05_317_pullx.xvg
                    3_05_36.tpr
                    3_05_36_pullx.xvg
                    3_05_444.tpr
                    3_05_444_pullx.xvg
                    3_05_494.tpr
                    3_05_494_pullx.xvg
                    3_05_592.tpr
                    3_05_592_pullx.xvg
                    3_05_63.tpr
                    3_05_63_pullx.xvg
                    3_05_707.tpr
                    3_05_707_pullx.xvg
                    3_05_864.tpr
                    3_05_864_pullx.xvg
                    3_05_96.tpr
                    3_05_96_pullx.xvg
                    3_1_0.tpr
                    3_1_0_pullx.xvg
                    3_1_132.tpr
                    3_1_132_pullx.xvg
                    3_1_159.tpr
                    3_1_159_pullx.xvg
                    3_1_160.tpr
                    3_1_160_pullx.xvg
                    3_1_169.tpr
                    3_1_169_pullx.xvg
                    3_1_176.tpr
                    3_1_176_pullx.xvg
                    3_1_289.tpr
                    3_1_289_pullx.xvg
                    3_1_312.tpr
                    3_1_312_pullx.xvg
                    3_1_32.tpr
                    3_1_32_pullx.xvg
                    3_1_375.tpr
                    3_1_375_pullx.xvg
                    3_1_4.tpr
                    3_1_41.tpr
                    3_1_41_pullx.xvg
                    3_1_430.tpr
                    3_1_430_pullx.xvg
                    3_1_454.tpr
                    3_1_454_pullx.xvg
                    3_1_4_pullx.xvg
                    3_1_527.tpr
                    3_1_527_pullx.xvg
                    3_1_561.tpr
                    3_1_561_pullx.xvg
                    3_1_591.tpr
                    3_1_591_pullx.xvg
                    3_1_622.tpr
                    3_1_622_pullx.xvg
                    3_1_696.tpr
                    3_1_696_pullx.xvg
                    3_1_790.tpr
                    3_1_790_pullx.xvg
                    3_1_806.tpr
                    3_1_806_pullx.xvg
                    3_1_857.tpr
                    3_1_857_pullx.xvg
                    3_1_86.tpr
                    3_1_86_pullx.xvg
                    3_1_872.tpr
                    3_1_872_pullx.xvg
                    3_1_914.tpr
                    3_1_914_pullx.xvg
                    3_1_95.tpr
                    3_1_95_pullx.xvg
                    analyze_umbrella_blocks.sh
                    analyze_umbrella_final.sh
                    bsProfs_100-120ns.xvg
                    bsProfs_120-140ns.xvg
                    bsProfs_140-160ns.xvg
                    bsProfs_160-180ns.xvg
                    bsProfs_180-200ns.xvg
                    bsProfs_20-40ns.xvg
                    bsProfs_40-60ns.xvg
                    bsProfs_60-80ns.xvg
                    bsProfs_80-100ns.xvg
                    bsProfs_80-200ns.xvg
                    bsResult_100-120ns.xvg
                    bsResult_120-140ns.xvg
                    bsResult_140-160ns.xvg
                    bsResult_160-180ns.xvg
                    bsResult_180-200ns.xvg
                    bsResult_20-40ns.xvg
                    bsResult_40-60ns.xvg
                    bsResult_60-80ns.xvg
                    bsResult_80-100ns.xvg
                    bsResult_80-200ns.xvg
                    frames.dat
                    histo_100-120ns.xvg
                    histo_120-140ns.xvg
                    histo_140-160ns.xvg
                    histo_160-180ns.xvg
                    histo_180-200ns.xvg
                    histo_20-40ns.xvg
                    histo_40-60ns.xvg
                    histo_60-80ns.xvg
                    histo_80-100ns.xvg
                    histo_80-200ns.xvg
                    profile_100-120ns.xvg
                    profile_120-140ns.xvg
                    profile_140-160ns.xvg
                    profile_160-180ns.xvg
                    profile_180-200ns.xvg
                    profile_20-40ns.xvg
                    profile_40-60ns.xvg
                    profile_60-80ns.xvg
                    profile_80-100ns.xvg
                    profile_80-200ns.xvg
                    pullx_files.dat
                    tpr_files.dat