GROMACS

Description

GROMACS is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers and fluid dynamics.

Read more on the GROMACS home page.

Strengths

• 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 uses any available GPUs. To achieve the best performance GROMACS uses both GPUs and CPUs in a reasonable balance.

QuickStart

Environment modules

The following versions have been installed:

Modules for running on CPUs

Modules for running on GPUs

*Release notes can be found here.

These modules can be loaded by using a module load command. Note that Intel MPI module file should be loaded first:

module load impi/2019.5 gromacs/2019.6

This provides access to the binary gmx_mpi which can be used to run simulations with sub-commands as gmx_mpi mdrun

In order to run simulations MPI runner should be used:

mpirun gmx_mpi mdrun MDRUNARGUMENTS

In order to load the GPU enabled version (avaiable only on the bgn nodes):

Modules can be loaded by using a module load command. Note that the following module files should be loaded first:

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

Submission script examples

Simple CPU 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.

#!/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 node CPU job script

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.

#!/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 script

Following script using four thread-MPI ranks. One is dedicated to the long-range PME calculation. Using the -gputasks 0001 keyword: the first 3 threads offload their short-range non-bonded calculations to the GPU with ID 0, the 4th (PME) thread offloads its calculations to the GPU with ID 1.

#!/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_tmpi
 
export GMX_GPU_DD_COMMS=true
export GMX_GPU_PME_PP_COMMS=true
 
OMP_NUM_THREADS=9
 
gmx mdrun -ntomp 9 -ntmpi 4 -nb gpu -pme gpu -npme 1 -gputasks 0001 OTHER MDRUNARGUMENTS

Whole node GPU job script

To setup a whole node GPU job use the -gputasks keyword.

#!/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_tmpi
 
export GMX_GPU_DD_COMMS=true
export GMX_GPU_PME_PP_COMMS=true
 
OMP_NUM_THREADS=9
 
gmx mdrun -ntomp 9 -ntmpi 16 -gputasks 0000111122223333 MDRUNARGUMENTS

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

GROMACS contains many tools that for analysing your results such as read trajectories (XTC, TNG or TRR format) as well as a coordinate file (GRO, PDB, TPR) and write plots in the XVG format. A list of commands with a short description can be find organised by topic at the official website.

VMD

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting, it is free of charge, and includes source code..

Python

Python packages, MDAnalysis and MDTraj, can read and write trajectory- and coordinate-files of GROMACS and both have a variety of used analysis functions. Both packages integrate well with Python’s data-science packages like NumPy, SciPy and Pandas, and with plotting libraries such as Matplotlib.

Usage tips

System preparation

Your tpr file (portable binary run input file) contains your initial structure, molecular topology and all of the simulation parameters. Tpr files are portable can be copied from one computer to another one, but you should always use the same version of mdrun and grompp. Mdrun is able to use tpr files that have been created with an older version of grompp, but this can cause unexpected results in your simulation.

Running simulations

Simulations often take longer time than the maximum walltime. By using mdrun with -maxh command will tell the program the requested walltime and GROMACS will finishes the simulation when reaching 99% of the walltime. At this time, mdrun creates a new checkpoint file and properly close all output files. Using this method, the simulation can be easily restarted from this checkpoint file.

mpirun gmx_mpi mdrun MDRUNARGUMENTS -maxh 24

Restarting simulations

In order to restart a simulation from checkpoint file you can use the same mdrun command as the original simulation and adding -cpi filename.cpt where the filename is the name of your most recent checkpoint file.

mpirun gmx_mpi mdrun MDRUNARGUMENTS -cpi filename.cpt

More detailed information can be find here.

Performance

GROMACS prints information about statistics and performance at the end of the md.log file which usually also contains helpful tips to further improve the performance. The performance of the simulation is usually given in ns/day (number if nanoseconds of MD-trajectories simulated within a day).

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

Special Performance Instructions for Emmy at GWDG

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.

Useful links

• GROMACS Manuals and documentation
• GROMACS Community Forums
• Useful MD Tutorials for GROMACS
• VMD Visual Molecular Dynamics

References

1. GROMACS User-Guide
2. PLUMED Home