Auszug |
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a versatile package to perform molecular dynamics for systems with hundreds to millions of particles. |
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- 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 the standard MPI communication protocol.
- 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.
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Version | Installation Path | modulefile | compiler | comment |
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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 |
2023.0 | /sw/chem/gromacs/2023.0/a100/tmpi | gromacs/2023.0 |
*Release notes can be find here.
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In order to load the GPU enabled version :Coming soon...(avaiable only on the bgn nodes):
Modules can be loaded by using a module load command. Note that the following module files should be loaded first:
module load gcc/11.3.0 intel/2023.0.0 cuda/11.8 gromacs/2023.0
Submission script examples
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More information about performance of the simulations and "how to imporve perfomance" can be find here.
Useful links
- GROMACS Manuals and documentation
- GROMACS Community Forums
- Useful MD Tutorials for GROMACS
- VMD Visual Molecular Dynamics