Introduction

Collective Molecular Dynamics is a VMD plugin GUI and a Python module developed for setup and analysis of simulations described in [MG13].

Installation

1. VMD 1.9.2 or later is required for using GUI. NAMD is required for running molecular dynamics simulations and latest version of ProDy is required for elastic network model calculations. Following are required for performing coMD calculations:

• Python 2.7
• NumPy 1.3 or later

2. Download one of the following archive files:

• comd_plugin_files.tgz
• comd_plugin_files.zip

3. Extract contents of the archive and copy comd folder to VMD TCL plugins directory, i.e. $VMDDIR/plugins/noarch/tcl/.

   Then, insert following line into $VMDDIR/scripts/vmd/loadplugins.tcl at line 200:

   vmd_install_extension comd comd_tk "Simulations/Collective Molecular Dynamics (CoMD)"
   

   If you are not sure where VMD directory is located, run vmd, and type the following command line in the VMD console:

   global env; puts $env(VMDDIR)
   

coMD Plugin

Collective Molecular Dynamics (coMD) plugin, shown below, has a panel to setup, collective molecular dynamics simulations:

The rest of the tutorial will show you how to use this panel, and described required inputs and outputs from analysis steps.

Tutorial Files

Files in the following archives can be used to follow this tutorial:

• coMD Tutorial Files (TGZ)
• coMD Tutorial Files (ZIP)

Here is a list of these files:

350K Feb 29 20:20 1ake.pdb
304K Feb 29 20:20 4ake.pdb
2.8M Feb 29 20:20 final_ionized.pdb
 17M Feb 29 20:20 final_trajectory.dcd
2.2M Feb 29 20:20 initial_ionized.pdb
 14M Feb 29 20:20 initial_trajectory.dcd

How to Cite

If you benefited from collective molecular dynamics in your research, please cite the following paper:

[MG13]

Gur M, Madura J, Bahar I Global Transitions of Proteins Explored by a Multiscale Hybrid Methodology: Application to Adenylate Kinase Biophys J 2013 7:1643–1652