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Auszug

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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VersionInstallation Pathmodulefilecompilercomment
Modules for running on CPUs 
2018.4/sw/chem/gromacs/2018.4/skl/impigromacs/2018.4intelmpi
2018.4/sw/chem/gromacs/2018.4/skl/impi-plumedgromacs/2018.4-plumedintelmpiwith plumed
2019.6/sw/chem/gromacs/2019.6/skl/impigromacs/2019.6intelmpi
2019.6/sw/chem/gromacs/2019.6/skl/impi-plumedgromacs/2019.6-plumedintelmpiwith plumed
2021.2/sw/chem/gromacs/2021.2/skl/impigromacs/2021.2intelmpi
2021.2/sw/chem/gromacs/2021.2/skl/impi-plumedgromacs/2021.2-plumedintelmpi

with plumed

Modules for running on GPUs

2023.0/sw/chem/gromacs/2023.0/a100/tmpi_gccgromacs/2023.0_tmpi 


*Release notes can be find here

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Note: Settings of the Thread-MPI ranks and OpenMP threads is for achieve optimal performance. The number of ranks should be a multiple of the number of sockets, and the number of cores per node should be a multiple of the number of threads per rank.

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 to run meta-dynamics simulations.

Analyzing results

GROMACS Tools

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More information about performance of the simulations and "how to imporve perfomance" can be find here


Useful links

References

  1. GROMACS User-Guide
  2. PLUMED Home