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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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#!/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.
Gromacs/20XX.X-plumed modules are versions have been patched with PLUMED's modifications, and these versions are able can 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
- GROMACS Manuals and documentation
- GROMACS Community Forums
- Useful MD Tutorials for GROMACS
- VMD Visual Molecular Dynamics