Parallel tempering (replica-exchange among temperatures) example using MPI-enabled repex.py.

AUTHOR

John D. Chodera <jchodera@berkeley.edu>

MANIFEST

thermodynamics.py - ThermodynamicState class definition
repex.py - definitions for ReplicaExchange, ParallelTempering, and HamiltonianExchange
hp35.pdb - PDB file for HP35 test system
hp35.inpcrd - initial coordinates for HP35 test system
hp35.prmtop - AMBER parameters for HP35 test system

PREREQUISITES

* OpenMM
* pyopenmm
* numpy
* netCDF4 + NetCDF + HDF5
* mpi4py (optional, to use MPI)
* scipy.weave (optional, for faster mixing)

USAGE

To run serially:

 python ParallelTemperingDriverMPI.py

To run on NCSA Forge, I used:

 # Start MPI daemon on the node (only have to do this once)
 mpd &
 # Run on six GPUs
 mpirun -np 6 python ParallelTemperingDriverMPI.py