GROMACS
Details on the GROMACS package. How to access, compile and run the program.
Useful Links
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
The default version of GROMACS on HECToR is 4.6.0.
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 HECToR 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 #PBS -l mppwidth=4096 #PBS -l mppnppn=32 #PBS -l walltime=00:05:00 # Replace this with your budget #PBS -A z01 # Move to directory that script was submitted from export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR) cd $PBS_O_WORKDIR # Set the number of threads to 1 # This prevents any system libraries from automatically # using threading. export OMP_NUM_THREADS=1 # Load the GROMACS module module add gromacs # Run NWChem using the input my_file.nw aprun -n 4096 -N 32 mdrun_mpi
