Large‐Scale Asynchronous and Distributed Multidimensional Replica Exchange Molecular Simulations and Efficiency Analysis
Junchao Xia, William F. Flynn, Emilio Gallicchio, Bin W. Zhang, Peng He, Zhiqiang Tan, Ronald M. Levy · Journal of Computational Chemistry · 2016
The ASyncRE methodology is presented, allowing the performance of large-scale replica exchange molecular dynamics (REMD) simulations asynchronously on grid computing networks consisting of heterogeneous and distributed computing environments, as well as on homogeneous high performance clusters like NSF XSEDE clusters and BOINC distributed computing networks at Temple University and Brooklyn College at CUNY. Several ways to improve the efficiency of REMD simulations in the context of the ASyncRE methodology are also proposed.