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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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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 simulationsSince the migration of the CPU partition from CentOS to Rocky 9 Linux, all GROMACS-PLUMED modules have now been combined with normal GROMACS modules. For example, to use GROMACS 2023.0 with PLUMED, one can load gromacs/2022.5 and have access to both normal (gmx_mpi) and PLUMED-patched (gmx_mpi_plumed) binaries.
PLUMED can be used to bias GROMACS simulations with an appropriate PLUMED data file supplied as input for the -plumed option for the gmx_mpi_plumed mdrun command:
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#!/bin/bash
#SBATCH --time=12:00:00
#SBATCH --partition=cpu-clx
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=72
export SLURM_CPU_BIND=none
module load gcc/11.3.0 cuda/11.8 openmpi/gcc.11/4.1.4
module load gromacs/2022.5
OMP_NUM_THREADS=9
mpiexec -np 4 -npernode 2 gmx_mpi mdrun -ntomp 9 -npme 1 -pin on -plumed plumed.dat OTHER MDRUNARGUMENTS |
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Not every GROMACS GPU option is compatible with PLUMED operations. For example, |
For additional information about PLUMED, please visit the official website.
Analyzing results
GROMACS Tools
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Turbo-boost has been mostly disabled on Emmy at GWDG (partitions medium40, large40, standard96, large96, and huge96) in order to save energy. However, this has a particularly strong performance impact on GROMACS in the range of 20-40%. Therefore, we recommend that GROMACS jobs be submitted requesting turbo-boost to be enabled with the --constraint=turbo_on option given to srun or sbatch.