GROMACS

Details on the GROMACS package. How to access, and run the program.

Useful Links

• GROMACS web page
• GROMACS documentation

Licensing

GROMACS is open source software.

Access

As it is open source software, the GROMACS source and binaries are available to all users.

Running

To run GROMACS you need to add the correct module to your environment. You can load the default GROMACS module with:

module add gromacs

Once you have added the module you will have access to the GROMACS executables in your path. The executables are classified according to the suffix. The available suffices on ARCHER are:

• _mpi_d - parallel, double-precision executables.
• _mpi - parallel, single-precision executables.
• _d - serial, double-precision executables.
• *no suffix* - serial, single-precision executables.

Example Job Submission Script

An example GROMACS job submission script is shown below.

#!/bin/bash --login
#PBS -N GROMACS_job

# Select 128 nodes (maximum of 3072 cores)
#PBS -l select=128

#PBS -l walltime=00:05:00

# Replace this with your budget code
#PBS -A budget

# Move to directory that script was submitted from
export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
cd $PBS_O_WORKDIR

# Load the GROMACS module 
module add gromacs

# Run GROMACS using default input and output file names
aprun -n 3072 mdrun_mpi

Compilation

• Compiling GROMACS for ARCHER (on GitHub)
• Adding PLUMED 2 Plugin to GROMACS 5.0.x

Compilation isntructions for older versions of GROMACS:

• Compiling GROMACS 4.6.x on ARCHER
• Adding PLUMED 2 Plugin to GROMACS 4.6.x