GROMACS

GROMACS is a free versatile package to perform molecular dynamics simulations (i.e. simulate the Newtonian equations of motion for molecular systems).

One version of GROMACS (4.6.7) is installed and primarily used by the Maibaum group in the Chemistry Department. This particular installation features the PLUMED-2.1.3 plug-in for metadynamics analysis. Both packages were built with impi support which enables parallelized simulation with or without PLUMED.

To properly use this installation of GROMACS, the user will have to load proper module files to set up the environment, which includes the GROMACS module itself:

module load contrib/gromacs_4.6.7-plumed_2.1.3-impi

as well as the proper mpi icc module with which the packages were built:

module load icc_15.0.3-impi_5.0.3

You should include both of those lines in your submission scripts.

This is an example of a line to include in your submission script in order to run the GROMACS jobs:

mpiexec.hydra -bootstrap rsh -rmk pbs mdrun -s input.tpr -deffnm output

The commands before mdrun are used to submit the job to the cluster and those after are GROMACS specific. This example uses the mdrun command, but it could be something else depending on what the user is trying to do. The grompp command was used to integrate all information into a binary file prior to the simulation. You can also use g_rdf, g_msd, and other g_XXX scripts to analyze the simulation afterward.

For this example, the -s and -deffnm are the flags specifying the input/output files for the mdrun command. A different command would have different flags available. One can always find out what a particular command does and what kind of flags to run it with by loading the module and then entering <command name> -h in the command line.

Note: The multi-processor support is built with default command names, so no “_mpi” affix is needed when calling a GROMACS function with this installation. For example, use mdrun instead of mdrun_mpi.