Gromacs

Description

From the Gromacs web site: GROMACS is a versatile package to perform molecular dynamics and energy minimization, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation, (check the online reference or manual for details), but there are also quite a few features that make it stand out from the competition.

Version

  • 2016.2

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

Gromacs requires the following module file to run:

  • apps/gromacs/2016.2

Running Gromacs on CIRCE/SC

The Gromacs user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Submitting Jobs

In order to start a simulation, you will need a protein or molecule to use. Go to http://www.rcsb.org/pdb/ and grab one in .pdb format. Follow the below procedure for simple molecules.

  1. Run pdb2gmx -f <pdb file> file(s).
  2. Run editconf with proper parameters to change the dimensions of the box.
  3. Run genbox with proper parameters to add solvate.
  4. Run grompp to pre-process your input data.
  • An additional file is needed for grompp called `grommp.mdp`. You can grab a copy of it from /apps/gromacs/4.5.5/share/gromacs/tutor/methanol and modify it in your local directory as needed.

The script below (for testing, name it “gromacs-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue. For help on submitting jobs to the queue, see our SLURM User’s Guide. Scripts are provided as examples only. Your SLURM executables, tools, and options will vary.

#!/bin/bash
#
#SBATCH --comment=gromacs-test
#SBATCH --ntasks=16
#SBATCH --job-name=gromacs-test
#SBATCH --output=output.%j.gromacs-test
#SBATCH --time=01:00:00

#### SLURM 16 processor Gromacs test to run for 1 hour.

module purge
module add apps/gromacs/2016

mpirun -np $SLURM_NTASKS gmx_mpi -v

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./gromacs-test.sh
  • You can view the status of your job with the “squeue -u <username>” command


Documentation

Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with Gromacs to the IT Help Desk: rc-help@usf.edu