Parallel tempering example with PyOpenMM + OpenMM.

MANIFEST

run-ParallelTemperingDriverMPI.sh - example batch script for NCSA Lincoln PBS queue for MPI execution
ParallelTemperingDriverMPI.py - python driver to run MPI version of parallel tempering
ParallelTemperingDriver.py - python driver to run serial version of parallel tempering
analze-parallel-tempering-schemes.py - cursory replica correlation time analysis
repexmpi.py - MPI-enabled (via mpi4py) replica-exchange package
repex.py - serial execution replica-exchange package

USAGE

On a PBS-enabled batch queue system, you can modify and submit or run the run-ParallelTemperingDriverMPI.sh.

This will create a NetCDF output file (*.nc) that stores the state of the calculation along with data generated from the simulation.

If execution is halted, re-running the script will detect whether the NetCDF file exists and back up to the last iteration to continue execution.  The NetCDF file should be deleted if execution from the beginning is desired.

Launching of the serial version can be done via:

python ParallelTemperingDriver.py

Refer to your system's local MPI implementation documentation for information on launching the MPI-enabled version ParallelTemperingDriverMPI.py.

Two systems are defined in the drivers ParallelTemperingDriver.py and ParallelTemperingDriverMPI.py: alanine dipeptide in implicit solvent and beta-lactalbumin in implicit solvent.  Uncomment the appropriate Amber prmtop/crd files as needed.

The analysis script simply does a cursory analysis of replica-correlation times.  Ask us if you need to do more sophisticated analysis, such as computing temperature-dependent properties or potentials of mean force.