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:
  1. Download one of the following archive files:
  1. 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 "Modeling/DruGUI"
    

    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:

../../_images/comd_gui_setup.png

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:

Here is a list of these files:

350K May 10 09:33 1ake.pdb
304K May 10 09:33 4ake.pdb
2.8M May 10 09:33 final_ionized.pdb
 17M May 10 09:33 final_trajectory.dcd
2.2M May 10 09:33 initial_ionized.pdb
 14M May 10 09:33 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