title: Greedy replica exchange algorithm for heterogeneous computing grids.
abstract: Replica exchange molecular dynamics (REMD) has become a valuable tool in studying complex biomolecular systems. However, its application on distributed computing grids is limited by the heterogeneity of this environment. In this study, we propose a REMD implementation referred to as greedy REMD (gREMD) suitable for computations on heterogeneous grids. To decentralize replica management, gREMD utilizes a precomputed schedule of exchange attempts between temperatures. Our comparison of gREMD against standard REMD suggests four main conclusions. First, gREMD accelerates grid REMD simulations by as much as 40 %. Second, gREMD increases CPU utilization rates in grid REMD by up to 60 %. Third, we argue that gREMD is expected to maintain approximately constant CPU utilization rates and simulation wall-clock times with the increase in the number of replicas. Finally, we show that gREMD correctly implements the REMD algorithm and reproduces the conformational ensemble of a short peptide sampled in our previous standard REMD simulations. We believe that gREMD can find its place in large-scale REMD simulations on heterogeneous computing grids.
authors: School of Systems Biology, George Mason University, Manassas, VA, 20110, USA.
authors: Christopher
authors: C
authors: Lockhart
authors: James
authors: J
authors: O'Connor
authors: Steven
authors: S
authors: Armentrout
authors: Dmitri K
authors: DK
authors: Klimov
mesh_terms: D000465:Algorithms; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry; D013696:Temperature
chemical_list: D010455:Peptides