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

Matthew C Zwier1, Joshua L Adelman, Joseph W Kaus

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

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|September 23, 2015
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Summary

The Weighted Ensemble (WE) simulation method enhances rare event sampling. WESTPA, a new open-source software package, enables scalable execution and analysis of WE simulations for diverse scientific problems.

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Area of Science:

  • Computational Chemistry
  • Biophysics
  • Systems Biology

Background:

  • Rare events in molecular and cellular systems are challenging to simulate.
  • Existing methods struggle with scalability and broad applicability.
  • Accurate simulation of molecular associations and conformational changes is crucial.

Purpose of the Study:

  • To introduce WESTPA, an open-source software package for Weighted Ensemble (WE) simulations.
  • To provide a scalable and interoperable platform for rare event simulation.
  • To facilitate the analysis of WE simulation data across various scales.

Main Methods:

  • Development of the WESTPA software package for WE simulations.
  • Implementation of parallelized trajectory replication and pruning strategies.
  • Integration with multiple molecular dynamics and cell modeling engines.

Main Results:

  • WESTPA demonstrates high scalability to thousands of CPU cores.
  • The software successfully interfaces with diverse simulation packages (GROMACS, NAMD, OpenMM, AMBER, BioNetGen, MCell).
  • WESTPA has been validated on problems from host-guest associations to cellular signaling networks.

Conclusions:

  • WESTPA provides a robust and scalable solution for rare event simulations.
  • The software enhances the study of complex molecular and cellular processes.
  • WESTPA's interoperability and analysis tools accelerate scientific discovery.