WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis

Matthew C. Zwier, Joshua L. Adelman, Joseph W. Kaus, Adam J. Pratt, Kim F. Wong, Nicholas B. Rego, Ernesto Suárez, Steven Lettieri, David W. Wang, Michael Grabe, Daniel Zuckerman, Lillian T. Chong

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

The weighted ensemble (WE) path sampling approach orchestrates an ensemble of parallel calculations with intermittent communication to enhance the sampling of rare events, such as molecular associations or conformational changes in proteins or peptides. Trajectories are replicated and pruned in a way that focuses computational effort on underexplored regions of configuration space while maintaining rigorous kinetics. To enable the simulation of rare events at any scale (e.g., atomistic, cellular), we have developed an open-source, interoperable, and highly scalable software package for the execution and analysis of WE simulations: WESTPA (The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis). WESTPA scales to thousands of CPU cores and includes a suite of analysis tools that have been implemented in a massively parallel fashion. The software has been designed to interface conveniently with any dynamics engine and has already been used with a variety of molecular dynamics (e.g., GROMACS, NAMD, OpenMM, AMBER) and cell-modeling packages (e.g., BioNetGen, MCell). WESTPA has been in production use for over a year, and its utility has been demonstrated for a broad set of problems, ranging from atomically detailed host-guest associations to nonspatial chemical kinetics of cellular signaling networks. The following describes the design and features of WESTPA, including the facilities it provides for running WE simulations and storing and analyzing WE simulation data, as well as examples of input and output.

Original languageEnglish (US)
Pages (from-to)800-809
Number of pages10
JournalJournal of Chemical Theory and Computation
Volume11
Issue number2
DOIs
StatePublished - Feb 10 2015
Externally publishedYes

Fingerprint

Software packages
Sampling
Cell signaling
computer programs
Reaction kinetics
Peptides
Program processors
Molecular dynamics
simulation
Trajectories
Engines
Proteins
Kinetics
Communication
sampling
data simulation
peptides
engines
reaction kinetics
communication

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

Cite this

Zwier, M. C., Adelman, J. L., Kaus, J. W., Pratt, A. J., Wong, K. F., Rego, N. B., ... Chong, L. T. (2015). WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis. Journal of Chemical Theory and Computation, 11(2), 800-809. https://doi.org/10.1021/ct5010615

WESTPA : An interoperable, highly scalable software package for weighted ensemble simulation and analysis. / Zwier, Matthew C.; Adelman, Joshua L.; Kaus, Joseph W.; Pratt, Adam J.; Wong, Kim F.; Rego, Nicholas B.; Suárez, Ernesto; Lettieri, Steven; Wang, David W.; Grabe, Michael; Zuckerman, Daniel; Chong, Lillian T.

In: Journal of Chemical Theory and Computation, Vol. 11, No. 2, 10.02.2015, p. 800-809.

Research output: Contribution to journalArticle

Zwier, MC, Adelman, JL, Kaus, JW, Pratt, AJ, Wong, KF, Rego, NB, Suárez, E, Lettieri, S, Wang, DW, Grabe, M, Zuckerman, D & Chong, LT 2015, 'WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis', Journal of Chemical Theory and Computation, vol. 11, no. 2, pp. 800-809. https://doi.org/10.1021/ct5010615
Zwier, Matthew C. ; Adelman, Joshua L. ; Kaus, Joseph W. ; Pratt, Adam J. ; Wong, Kim F. ; Rego, Nicholas B. ; Suárez, Ernesto ; Lettieri, Steven ; Wang, David W. ; Grabe, Michael ; Zuckerman, Daniel ; Chong, Lillian T. / WESTPA : An interoperable, highly scalable software package for weighted ensemble simulation and analysis. In: Journal of Chemical Theory and Computation. 2015 ; Vol. 11, No. 2. pp. 800-809.
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