Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 11, Issue 2, Pages 800-809Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ct5010615
Keywords
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Funding
- NSF CAREER [MCB-0845216]
- Office of the Provost at Drake University
- National Institutes of Health (NIH) [R01-GM089740]
- NIH [T32-DK061296, P41 GM103712]
- NSF [MCB-1119091]
- University of Pittsburgh Arts & Sciences Graduate, Department of Chemistry Graduate Excellence
- University of Pittsburgh Andrew Mellon Fellowships
- University of Pittsburgh Brackenridge Fellowship
- NSF XSEDE [MCB-100109]
- NSF MRI [CNS-1229064]
- Division Of Computer and Network Systems
- Direct For Computer & Info Scie & Enginr [1229064] Funding Source: National Science Foundation
- Div Of Molecular and Cellular Bioscience
- Direct For Biological Sciences [0845216] Funding Source: National Science Foundation
- Div Of Molecular and Cellular Bioscience
- Direct For Biological Sciences [1119091] Funding Source: National Science Foundation
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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 hostguest 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.
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