Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD

Wei Jiang, James C. Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James C. Gumbart, Yun Luo, Klaus Schulten, Benoît Roux

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)908-916
Number of pages9
JournalComputer Physics Communications
Volume185
Issue number3
DOIs
StatePublished - Mar 1 2014

Keywords

  • Charm++
  • MCA
  • NAMD
  • Tcl

ASJC Scopus subject areas

  • Hardware and Architecture
  • Physics and Astronomy(all)

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    Jiang, W., Phillips, J. C., Huang, L., Fajer, M., Meng, Y., Gumbart, J. C., Luo, Y., Schulten, K., & Roux, B. (2014). Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD. Computer Physics Communications, 185(3), 908-916. https://doi.org/10.1016/j.cpc.2013.12.014