Difference between revisions of "Gromacs"
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Revision as of 18:48, 1 August 2016
Description
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.
Citation
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)
