GROMACS

Overview

GROMACS is a full-featured suite of programs to perform molecular dynamics simulations, i.e., to simulate the behavior of systems with hundreds to millions of particles using Newtonian equations of motion. It is primarily used for research on proteins, lipids, and polymers, but can be applied to a wide variety of chemical and biological research questions.

Availability

Cluster	Module/Version
BOSE	test-gromacs/2024.3
BGSC	Not Available

Note: You can simply use module load test-gromacs to activate the most recently installed version of this software.

Arguments / Options

This is a list of arguments for the GROMACS command that we wanted to highlight. Use man gmx or this online man page for a full list.

Option	Description
-h	Print help and quit
-version	Print extended version information and quit
help commands	List of available commands

Sample Slurm Script

submit.sh

#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]

# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32     # How many CPU cores do you want to request
#SBATCH --nodes=1                # How many nodes do you want to request

# -- SCRIPT COMMANDS -- #

# Load the needed modules
module load test-gromacs    # Load GROMACS
gmx [commands]

Real Example

Has your research group used GROMACS in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Please include the following citation in your papers to support continued development of GROMACS.

H. Bekker, H.J.C. Berendsen, E.J. Dijkstra, S. Achterop, R. van Drunen, D. van der Spoel, A. Sijbers, and H. Keegstra et al., “Gromacs: A parallel computer for molecular dynamics simulations”; pp. 252–256 in Physics computing 92. Edited by R.A. de Groot and J. Nadrchal. World Scientific, Singapore, 1993.
H.J.C. Berendsen, D. van der Spoel, and R. van Drunen, “GROMACS: A message-passing parallel molecular dynamics implementation,” Comp. Phys. Comm., 91 43–56 (1995).
E. Lindahl, B. Hess, and D. van der Spoel, “GROMACS 3.0: A package for molecular simulation and trajectory analysis,” J. Mol. Mod., 7 306–317 (2001).
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark, and H.J.C. Berendsen, “GROMACS: Fast, Flexible and Free,” J. Comp. Chem., 26 1701–1718 (2005).
B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, “GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation,” J. Chem. Theory Comput., 4 [3] 435–447 (2008).
S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M.R. Shirts, and J.C. Smith et al., “GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit,” Bioinformatics, 29 [7] 845–854 (2013).
S. Páll, M.J. Abraham, C. Kutzner, B. Hess, and E. Lindahl, “Tackling exascale software challenges in molecular dynamics simulations with GROMACS”; pp. 3–27 in Solving software challenges for exascale. Edited by S. Markidis and E. Laure. Springer International Publishing Switzerland, London, 2015.
M.J. Abraham, T. Murtola, R. Schulz, S. Páll, J.C. Smith, B. Hess, and E. Lindahl, “GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers,” SoftwareX, 1–2 19–25 (2015).