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DescriptionGROMACS is a versatile package to perform molecular dynamics 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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- 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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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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Submission scripts examples
Simple job script
A simple case of a GROMACS job using a total of 640 CPU cores for 12 hours. The requested amount of cores in the example does not include all available cores on the allocated nodes. The job will execute 92 ranks on 3 nodes + 91 ranks on 4 nodes. You can use this example if you know the exact amount of required ranks you want to use.
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#!/bin/bash #SBATCH -t 12:00:00 #SBATCH -p standard96 #SBATCH -n 640 export SLURM_CPU_BIND=none module load impi/2019.5 module load gromacs/2019.6 mpirun gmx_mpi mdrun MDRUNARGUMENTS |
Whole nodes
In case you want to use all cores on the allocated nodes, there are another options of the batch system to request the amount of nodes and number of tasks. The example below will result in running 672 ranks.
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#!/bin/bash #SBATCH -t 12:00:00 #SBATCH -p standard96 #SBATCH -N 7 #SBATCH --tasks-per-node 96 export SLURM_CPU_BIND=none module load impi/2019.5 module load gromacs/2019.6 mpirun gmx_mpi mdrun MDRUNARGUMENTS |
GPU job
coming soon...
Related Modules
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PLUMED is an open-source, community-developed library that provides a wide range of different methods, such as enhanced-sampling algorithms, free-energy methods and tools to analyze the vast amounts of data produced by molecular dynamics (MD) simulations. PLUMED works together with some of the most popular MD engines.
Gromacs/20XX.X-plumed modules are versions have been patched with PLUMED's modifications, and these versions are able can run meta-dynamics simulations.