Topics Map > Services > Research Computing and Support > CCAST
Running Gromacs on CCAST Clusters
This document describes basic usage of GROMACS on CCAST clusters. Far more information about GROMACS is available in the GROMACS manual, which is available online and is maintained by the GROMACS developers.
GROMACS is a free and open-source high-performance molecular dynamics package, mainly designed for simulations of proteins, lipids, and nucleic acids, but it is also used in simulation of drug design and polymers. On CCAST, GROMACS can be run on Thunder Prime using both CPU and/or GPU via the
The main executable for GROMACS is
gmx command can be used to run a variety of different tasks, including energy minimization, molecular dynamics, and analysis of output.
Running an Example Job
Example GROMACS job scripts are available in
/mmfs1/projects/ccastest/examples/GROMACS_example/. The example script that uses GPU acceleration is
job_gpu.pbs while the CPU-only script is
job_cpu.pbs. Both jobs take the
input.tpr file as input, which specifies a steepest descent energy minimization of the lysozyme protein in water (taken from a much more detailed GROMACS Tutorial by Justin A. Lemkul, PhD). The provided GROMACS example PBS scripts can be copied to your scratch directory and modified to suit your own needs.
Reading the Input File
GROMACS_example directory to your scratch directory.
$ cp -r /mmfs1/projects/ccastest/examples/GROMACS_example $SCRATCH/
$ cd $SCRATCH/GROMACS_example
You can view the contents of the
input.tpr file, use the
gmx dump command as follows:
$ gmx dump -s input.tpr | less
Submitting mdrun Jobs
To run the job, use the
qsub command as follows:
$ qsub job_cpu.pbs
The same job can also be run on the GPU-accelerated nodes by using the
job_gpu.pbs script instead.
$ qsub job_gpu.pbs
The job will take a few moments to run.
Working with GROMACS output files
Once it is complete, you can view the output files. The
gmx energy command can be used to read the
ener.edr file created.
$ gmx energy -f ener.edr -o potential.xvg
Opened ./ener.edr as single precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
1 Bond 2 Angle 3 Proper-Dih. 4 Ryckaert-Bell.
5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR)
9 Coul.-recip. 10 Potential 11 Pressure 12 Vir-XX
13 Vir-XY 14 Vir-XZ 15 Vir-YX 16 Vir-YY
17 Vir-YZ 18 Vir-ZX 19 Vir-ZY 20 Vir-ZZ
21 Pres-XX 22 Pres-XY 23 Pres-XZ 24 Pres-YX
25 Pres-YY 26 Pres-YZ 27 Pres-ZX 28 Pres-ZY
29 Pres-ZZ 30 #Surf*SurfTen 31 T-rest
> 10 0
Here, we select Potential, which is term
10. The output is written to
potential.xvg, which contains tabular data of the potential energy over the minimization.