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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 and fluid dynamics.
Read more on the GROMACS home page.
For a manual consult the the GROMACS home page.
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Strengths
- GROMACS provides extremely high performance compared to all other programs.
- GROMACS can make simultaneous use of both CPU and GPU available in a system. There are options to statically and dynamically balance the load between the different resources.
- GROMACS is user-friendly, with topologies and parameter files written in clear text format.
- Both run input files and trajectories are independent of hardware endian-ness, and can thus be read by any version GROMACS.
- GROMACS comes with a large selection of flexible tools for trajectory analysis.
- GROMACS can be run in parallel, using either the standard MPI communication protocol, or via our own “Thread MPI” library for single-node workstations.
- GROMACS contains several state-of-the-art algorithms.
- GROMACS is Free Software, available under the GNU Lesser General Public License (LGPL).
Weaknesses
- GROMACS does not do to much further analysis to get very high simulation speed.
- Sometimes it is challenging to get non-standard information about the simulated system.
- Different versions sometimes have differences in default parameters/methods. Reproducing older version simulations with a newer version can be difficult.
- Additional tools and utilities provided by GROMACS are sometimes not the top quality.
GPU support
Coming soon…
QuickStart
Environment modules
The following versions have been installed:
| Version | Installation Path | modulefile | compiler | comment |
|---|---|---|---|---|
| 2018.4 | /sw/chem/gromacs/2018.4/skl/impi | gromacs/2018.4 | intelmpi | |
| 2018.4 | /sw/chem/gromacs/2018.4/skl/impi-plumed | gromacs/2018.4-plumed | intelmpi | with plumed |
| 2019.6 | /sw/chem/gromacs/2019.6/skl/impi | gromacs/2019.6 | intelmpi | |
| 2019.6 | /sw/chem/gromacs/2019.6/skl/impi-plumed | gromacs/2019.6-plumed | intelmpi | with plumed |
| 2021.2 | /sw/chem/gromacs/2021.2/skl/impi | gromacs/2021.2 | intelmpi | |
| 2021.2 | /sw/chem/gromacs/2021.2/skl/impi-plumed | gromacs/2021.2-plumed | intelmpi | with plumed |
Usage
Load the necessary modulefiles. Note that Intel MPI module file should be loaded first
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These modules can be loaded by using a module load command. Note that Intel MPI module file should be loaded first:module load impi/2019.5 gromacs/2019.6
This provides access to the binary gmx_mpi wich can be used to run simulations with sub-commands as gmx_mpi mdrun
In order to run simulations MPI runner should be used:
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