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A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. |
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| 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 |
These
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modules
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can
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be
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loaded
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by
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using
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a
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module
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load
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command.
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Note
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that
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Intel
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MPI
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module
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file
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should
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be
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loaded
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first:
module load impi/2019.5 gromacs/2019.6
This
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provides
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access
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to
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the
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binary
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gmx_mpi
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wich
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can
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be
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used
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to
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run
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simulations
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with
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sub-commands
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as
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gmx_mpi
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mdrun
In order to run simulations MPI runner should be used:
mpirun gmx_mpi mdrun MDRUNARGUMENTS
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In order to load the GPU enabled version:
Coming soon...
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.
| Codeblock | ||||
|---|---|---|---|---|
| ||||
#!/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.
| Codeblock | ||||
|---|---|---|---|---|
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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
Gromacs-Plumed
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.