coMD is a VMD plugin GUI and a Python module developed for setup and analysis of simulations described in Gur et al., 2013.
http://prody.csb.pitt.edu/comd/
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