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J Chem Theory Comput. 2015 Feb 10;11(2):800-9. doi: 10.1021/ct5010615.

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

Author information

1
Department of Chemistry, Drake University, Des Moines, Iowa 50311, United States

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.

PMID:
26392815
PMCID:
PMC4573570
DOI:
10.1021/ct5010615
[Indexed for MEDLINE]
Free PMC Article

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