Skip to content

Python replica-exchange simulation facility for OpenMM.

License

Notifications You must be signed in to change notification settings

kyleabeauchamp/repex

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Build Status

repex

Replica-exchange simulation algorithms for OpenMM.

Description

This package provides a general facility for running replica-exchange simulations, as well as derived classes for special cases such as parallel tempering (in which the states differ only in temperature) and Hamiltonian exchange (in which the state differ only by potential function).

Simulations utilize a generic Markov chain Monte Carlo (MCMC) framework that makes it easy to mix Monte Carlo and molecular dynamics.

Provided classes include:

  • ReplicaExchange - Base class for general replica-exchange simulations among specified ThermodynamicState objects
  • ParallelTempering - Convenience subclass of ReplicaExchange for parallel tempering simulations (one System object, many temperatures/pressures)
  • HamiltonianExchange - Convenience subclass of ReplicaExchange for Hamiltonian exchange simulations (many System objects, same temperature/pressure)

Dependencies

Use of this module requires the following:

Authors

License

All code in this repository is released under the GNU Lesser General Public License. See LICENSE for details. Written by the authors at the University of California Berkeley and the Memorial Sloan-Kettering Cancer Center.

About

Python replica-exchange simulation facility for OpenMM.

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published