Molecular dynamics simulation primer for: Introduction to atomistic modeling and simulation of biomolecular systems
Data files
May 30, 2023 version files 500.53 MB
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kcsa_wt_1k4c_popc_namd01.zip
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README.md
Abstract
Molecular dynamics (MD) and related techniques have been used for computer simulations of biomolecular systems for over 40 years, but only recently due to advances in computer hardware, simulation software and methodologies, as well as breakthroughs in structural biology, have they become a widely-used tool for studying the molecular mechanisms of biological function and its modulation. This dataset represents a primer for learning basic MD simulation setup and analysis using a prototypical K+ channel KcsA embedded in a hydrated lipid bilayer. The dataset includes files necessary for setup of MD simulations using CHARMM-GUI web toolkit, running them using nanoscale MD (NAMD) and analysing using visual MD (VMD) sofware. Detailed explanations are provided in the book chapter "Introduction to Atomistic Modeling and Simulation of Biomolecular Systems" to be published soon.
Methods
The dataset was generated using CHARMM-GUI online toolkit to build a system for molecular dynamics (MD) simulations using K+ channel KcsA PDB ID: 1K4C crystal structure as an input. The protein was embedded in a POPC lipid bilayer solvated by aqueous 0.15 M KCl solution. Molecular system coordinate, topology and force field parameter files were generated along with input files for several popular MD simulation packages such as NAMD, Amber, Gromacs OpenMM, etc. CHARMM36m protein, C36 lipid force fields and TIP3P water model were used for MD simulations. NAMD software was used to run ~102 ns long MD simulation with the first 2 ns used as a restrained equilibration and subsequent 100 ns as a restraint-free production MD run. VMD software Tcl scripts were used to combine original NAMD binary trajectories and save them using 1 ns frequency and also fix issues with periodic boundary condition (PBC) protein image centering. VMD software was also used to perform multiple MD simulation analyses such as inter-residue distances, root-mean-square deviations (RMSD) and fluctuations (RMSF) of protein atoms. Analysis scripts, data files, plotting scripts and images are provided in the dataset as well.
Usage notes
CHARMM-GUI membrane builder (https://www.charmm-gui.org/?doc=input/membrane.bilayer ) was used for simulation system setup. Nanoscale molecular dynamics (NAMD) is needed to run MD simulations with other options (Gromacs, Amber, etc.) possible as well. Visual molecular dynamics (VMD) software is needed to perform MD simulation analysis. Both NAMD (http://www.ks.uiuc.edu/Research/namd/) and VMD (https://www.ks.uiuc.edu/Research/vmd/) are available free of charge for academic users.