Introduction
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 .
Installation
- VMD 1.9.1 or later is suggested for the generation of the files required for the communication between VMD and NAMD.
- NAMD is required for running the all atomic Molecular Dynamics simulations; Targeted Molecular Dynamics and Minimization.
- 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.
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