Difference between revisions of "Gromacs"

Jump to navigation Jump to search
Line 62: Line 62:
<!--PBS scripts-->
<!--PBS scripts-->
{{#if: {{#var: pbs}}|==PBS Script Examples==
{{#if: {{#var: pbs}}|==PBS Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
See the [[{{PAGENAME}}_SBATCH]] page for {{#var: app}} SBATCH script examples.

Revision as of 18:48, 1 August 2016


Gromacs website  

GROMACS is a versatile package to perform molecular dynamics, 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.

Required Modules

You must load the appropriate modules in your submission script.

Parallel (MPI)

  • intel/2016.0.109
  • openmpi/1.10.2
  • {{#lowercase:Gromacs}}

System Variables

  • HPC_GROMACS_DIR - installation directory
  • HPC_GROMACS_BIN - executable directory
  • HPC_GROMACS_INC - header file directory
  • HPC_GROMACS_LIB - library directory

PBS Script Examples

See the Gromacs_SBATCH page for Gromacs SBATCH script examples.


If you publish research that uses Gromacs you have to cite it as follows:
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation Hess, B., Kutzner, C., van der Spoel, D. and Lindahl, E. J. Chem. Theory Comput., 4, 435-447 (2008)