gromacs-plumx

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. (Summary from the program web page.)

The official web page:http://www.gromacs.org/

This version includes support for the PLUM force field created by Tristan Bereau from the Deserno group at CMU.

Notes:

All the necessary data and example files for the PLUM force field can be found in $PLUMDATA, see the section "Simulation setup" in $PLUMDATA/README for details and instructions how to set up a simulation. You can ignore the part about "source.me" and "GMX_NBLISTCG", everything is is already configured by the module. Do not put "./" in front of the names of PLUM helper scripts, they are installed in executable path.

The package supports sequential and parallel execution (see manual for details). The mdrun program was updated to automatically select the number of CPUs according to psubmit command.

Example script

#!/usr/bin/env infinity-env

module add gromacs-plumx

mdrun -s md1.tpr

Job submission as a single CPU job

$ psubmit normal test_me             # gromacs mdrun execution on 1 CPU

Job submission as a parallel job

$ psubmit normal test_me 8           # gromacs mdrun execution on 8 CPUs