Versionen im Vergleich

Schlüssel

  • Diese Zeile wurde hinzugefügt.
  • Diese Zeile wurde entfernt.
  • Formatierung wurde geändert.


Auszug

a versatile package to perform molecular dynamics for systems with hundreds to millions of particles.

...

  • 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.

GPU support

...

GROMACS automatically use any available GPUs.

QuickStart

Environment modules

...

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/tmpigromacs/2023.0


...

Codeblock
languagebash
linenumberstrue
#!/bin/bash 
#SBATCH --time=12:00:00
#SBATCH --partition=gpu-a100
#SBATCH --ntasks=72

export SLURM_CPU_BIND=none

module load gcc/11.3.0 intel/2023.0.0 cuda/11.8
module load gromacs/2023.0

export GMX_GPU_DD_COMMS=true
export GMX_GPU_PME_PP_COMMS=true

OMP_NUM_THREADS=9

gmx mdrun -ntomp 9 MDRUNARGUMENTS

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.

...

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