coMD is a methodology to generate all atomic transition pathways between any two structures/substates of a protein (described in MG9). The coMD script utilizes SHell , VMD , NAMD and MATLAB .


  1. VMD 1.9.1 or later is suggested for the generation of the files required for the communication between VMD and NAMD.
  2. NAMD is required for running the all atomic Molecular Dynamics simulations; Targeted Molecular Dynamics and Minimization.
  3. MATLAB is required for running the Coarse Grained MC/Metropolis simulations.

Since the aim is to simulate large systems we suggest to install all of these programs on a cluster/supercomputer. Please refer to the the schematic figure (Figure 2 in the Paper) below for a visual description where each program is required.


Figure 1: Schematic Description of coMD

The programs that are used to excecute each part are shown in the figure

How to Cite

If you benefited from coMD in your research, please cite the following paper:

[MG9] Gur M, Madura J D, and Bahar I. DGlobal Transitions of Proteins Explored by a Multiscale Hybrid Methodology: Application to Adenylate Kinase
Biophysical Journal, Volume 105, Issue 7, 1643-1652, 1 October 2013

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