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Comput Phys Commun. 2014 Mar;185(3):908-916.

Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD.

Author information

1
Argonne Leadership Computing Facility, Argonne National Laboratory, 9700 South Cass Avenue, Building 240, Argonne, Illinois 60439.
2
Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.
3
Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, 929 57th Street, Chicago, Illinois 60637.
4
Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, Illinois 60439 ; School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332.
5
Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 ; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.
6
Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, Illinois 60439 ; Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, 929 57th Street, Chicago, Illinois 60637.

Abstract

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/λ-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/λ-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.

KEYWORDS:

MCA; NAMD; Tcl; charm++

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