prody / coMD

This package runs collective molecular dynamics simulations, where collective motions from anisotropic network model normal mode analysis drive all-atom dynamics through targeted molecular dynamics simulations and energy minimization

http://prody.csb.pitt.edu/comd/

MIT License

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coMD

coMD is a VMD plugin GUI and a Python module developed for setup and analysis of simulations described in Gur et al., 2013.

Homepage

http://prody.csb.pitt.edu/comd/

Citation

Gur, M., Madura, J. D., & Bahar, I. (2013). Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase. Biophysical journal, 105(7), 1643-1652.

Paper: http://www.sciencedirect.com/science/article/pii/S000634951300934X