MDdMD: Maxwell-Demon discrete Molecular Dynamics
We present a new method for estimating pathways for conformational transitions in macromolecules from the use of discrete molecular dynamics and biasing techniques based on a combination of essential dynamics and Maxwell–Demon sampling techniques. The method can work with high efficiency at different levels of resolution, including the atomistic one, and can help to define initial pathways for further exploration by means of more accurate atomistic molecular dynamics simulations. The method is implemented in a freely available Web-based application accessible at https://mmb.irbbarcelona.org/MDdMD.
Pedro Sfriso, Agusti Emperador, Laura Orellana, Adam Hospital, Josep Lluis Gelpi and Modesto Orozco.
Finding conformational pathways from discrete molecular dynamics simulations.
J. Chem. Theory Comput., 2012, 8(11): 4707-4718.