期刊
COMPUTER PHYSICS COMMUNICATIONS
卷 185, 期 3, 页码 908-916出版社
ELSEVIER
DOI: 10.1016/j.cpc.2013.12.014
关键词
MCA; NAMD; Tcl; Charm plus
资金
- Office of Science of the U.S. Department of Energy [DE-AC02-06CH11357]
- National Institutes of Health [9P41GM104601, U54GM087519, K22-AI100927]
- National Science Foundation (NSF) [MCB-0920261]
- Early Science Program of Argonne Leadership Computing Facility
- Department of Energy Office of Science and used resources of the Argonne Leadership Computing Facility at Argonne National Laboratory
- Direct For Computer & Info Scie & Enginr
- Office of Advanced Cyberinfrastructure (OAC) [0832673, 1440026] Funding Source: National Science Foundation
Computational methodologies that couple the dynamical evolution of a set of replicated copies of a system of interest offer powerful and flexible approaches to characterize complex molecular processes. Such multiple copy algorithms (MCAs) can be used to enhance sampling, compute reversible work and free energies, as well as refine transition pathways. Widely used examples of MCAs include temperature and Hamiltonian-tempering replica-exchange molecular dynamics (T-REMD and H-REMD), alchemical free energy perturbation with lambda replica-exchange (FEP/lambda-REMD), umbrella sampling with Hamiltonian replica exchange (US/H-REMD), and string method with swarms-of-trajectories conformational transition pathways. Here, we report a robust and general implementation of MCAs for molecular dynamics (MD) simulations in the highly scalable program NAMD built upon the parallel programming system Charm++. Multiple concurrent NAMD instances are launched with internal partitions of Charm++ and located continuously within a single communication world. Messages between NAMD instances are passed by low-level point-to-point communication functions, which are accessible through NAMD's Tcl scripting interface. The communication-enabled Tcl scripting provides a sustainable application interface for end users to realize generalized MCAs without modifying the source code. Illustrative applications of MCAs with fine-grained inter-copy communication structure, including global lambda exchange in FEP/lambda-REMD, window swapping US/H-REMD in multidimensional order parameter space, and string method with swarms-of-trajectories were carried out on IBM Blue Gene/Q to demonstrate the versatility and massive scalability of the present implementation. Published by Elsevier B.V.
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