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Gromacs

Gromacs is a very efficient engine to perform molecular dynamics simulations and energy minimizations particularly for proteins. However, it can also be used to model polymers, membranes and e.g. coarse grained systems. It also comes with plenty of analysis scripts.

• Gromacs
  • Available
  • License
  • Usage
    • Notes about performance
    • Example parallel batch script for Puhti
    • Example serial batch script for Puhti
    • Example mpi-only parallel batch script for Mahti
    • Example mixed parallel batch script for Mahti
    • High-throughput computing with Gromacs
    • Visualizing trajectories and graphs
  • References
  • More information

Available

• Puhti: 2018-2022 releases with regularly updated minor versions, several with plumed or cuda
• Mahti: 2020-2022 releases with regularly updated minor versions, one with plumed, one with CP2K
• Check recommended version(s) with module avail gromacs-env
• If you want to use command-line plumed tools, load the plumed module.

Note

We only provide the parallel version gmx_mpi, but it can be used for grompp, editconf etc. similarly to the serial version. Instead of gmx grompp ... give gmx_mpi grompp

Note

CP2K 9.1 has been linked to Gromacs 2022 for QM/MM in the module gromacs-env/2022-cp2k on Mahti. This option was previously available under the CP2K module cp2k/8.1-gmx, which has now been deprecated. Please use gromacs-env/2022-cp2k for QM/MM simulations from now on. See the official documentation for more details.

License

Gromacs is free software available under LGPL, version 2.1.

Usage

Initialise recommended version of Gromacs on Puhti like this:

module purge
module load gromacs-env

Use module spider to locate other versions. To load these modules, you need to first load its dependencies, which are shown with module spider gromacs/version.

Notes about performance

It is important to set up the simulations properly to use resources efficiently. The most important are:

• If you run in parallel, make a scaling test for each system - don't use more cores than is efficient. Scaling depends on many aspects of your system and used algorithms, not just size.
• Use a recent version - there has been significant speedup over the years
• Minimize unnecessary disk I/O - never run batch jobs with -v (the verbose flag) for mdrun
• For large jobs, use full nodes (multiples of 40 cores, on Puhti) see example below.

For a more complete description, consult the mdrun performance checklist on the Gromacs page.

We recommend using the latest versions as they have most bugs fixed and tend to be faster. If you switch the major version, check that the results are comparable.

A scaling test with a very large system (1M+ particles) may take a while to load balance optimally. It's better to increase the number of nodes in your production simulation, IF you see better performance than in the scaling test at the scaling limit, rather than run very long scaling tests in advance.

Example parallel batch script for Puhti

#!/bin/bash
#SBATCH --time=00:15:00
#SBATCH --partition=large
#SBATCH --ntasks-per-node=40
#SBATCH --nodes=2
#SBATCH --account=<project>
##SBATCH --mail-type=END #uncomment to get mail

# this script runs a 80 core (2 full nodes) gromacs job, requesting 15 minutes time

module purge
module load gromacs-env
export OMP_NUM_THREADS=1

srun gmx_mpi mdrun -s topol -maxh 0.2 -dlb yes

Note

To avoid multi node parallel jobs to spread over more nodes than necessary, don't use the --ntasks flag, but specify --nodes and --ntasks-per-node=40 to get full nodes. This minimizes communication overhead and fragmentation of node reservations. Don't use the large partition for jobs with less than 40 cores.

Example serial batch script for Puhti

#!/bin/bash
#SBATCH --time=00:15:00
#SBATCH --partition=small
#SBATCH --ntasks=1
#SBATCH --account=<project>
##SBATCH --mail-type=END #uncomment to get mail

# this script runs a 1 core gromacs job, requesting 15 minutes time

module purge
module load gromacs-env
export OMP_NUM_THREADS=1

srun gmx_mpi mdrun -s topol -maxh 0.2

Note

Please make sure that using one GPU (and upto 10 cores) is at least twice as fast as using one full node of CPU cores according to the usage policy. Otherwise, don't use GPUs.

Submit the script with sbatch script_name.sh

Example mpi-only parallel batch script for Mahti

#!/bin/bash
#SBATCH --time=00:15:00
#SBATCH --partition=medium
#SBATCH --ntasks-per-node=128
#SBATCH --nodes=2
#SBATCH --account=<project>
##SBATCH --mail-type=END #uncomment to get mail

# this script runs a 256 core (2 full nodes, no hyperthreading) gromacs job, requesting 15 minutes time

module purge
module load gcc/9.4.0 openmpi/4.1.2 gromacs/2021.5

export OMP_NUM_THREADS=1

srun gmx_mpi mdrun -s topol -maxh 0.2 -dlb yes

Example mixed parallel batch script for Mahti

#!/bin/bash
#SBATCH --time=00:15:00
#SBATCH --partition=medium
#SBATCH --ntasks-per-node=64
#SBATCH --cpus-per-task=2
#SBATCH --nodes=2
#SBATCH --account=<project>
##SBATCH --mail-type=END #uncomment to get mail

# this script runs a 256 core (2 full nodes, no hyperthreading) gromacs job, requesting 15 minutes time
# 64 tasks per node, each with 2 OpenMP threads

module purge
module load gcc/9.4.0 openmpi/4.1.2 gromacs/2021.5

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

srun gmx_mpi mdrun -s topol -maxh 0.2 -dlb yes

High-throughput computing with Gromacs

Gromacs comes with a built-in multidir functionality, which allows users to run multiple concurrent simulations within one Slurm allocation. This is an excellent option for high-throughput use cases, where the aim is to run several similar, but independent, jobs. Notably, multiple calls of sbatch or srun are not needed, which decreases the load on the batch queue system. Please consider this option if you're running high-throughput workflows or jobs such as replica exchange, umbrella sampling or adaptive weight histogram (AWH) free energy simulations using Gromacs.

An example multidir.sh batch script for running a multidir Gromacs job is provided below. This example adapts the production part of the lysozyme tutorial by considering 8 similar copies of the system that have been equilibrated with different velocity initializations. Inputs corresponding to each copy are named identically md_0_1.tpr and placed in subdirectories run* as illustrated below by the output of the tree command.

$ tree
.
├── multidir.sh
├── run1
│   └── md_0_1.tpr
├── run2
│   └── md_0_1.tpr
├── run3
│   └── md_0_1.tpr
├── run4
│   └── md_0_1.tpr
├── run5
│   └── md_0_1.tpr
├── run6
│   └── md_0_1.tpr
├── run7
│   └── md_0_1.tpr
└── run8
    └── md_0_1.tpr

#!/bin/bash
#SBATCH --time=00:30:00
#SBATCH --partition=medium
#SBATCH --ntasks-per-node=128
#SBATCH --nodes=1
#SBATCH --account=<project>

# this script runs a 128 core gromacs multidir job (8 simulations, 16 cores per simulation)

module purge
module load gcc/9.4.0 openmpi/4.1.2 gromacs/2021.5

export OMP_NUM_THREADS=1

# Create a list of the directories, convenient if there are many
list=()
for i in `seq 8`
do
    list+=(run${i})
done

srun gmx_mpi mdrun -multidir ${list[@]} -deffnm md_0_1 -dlb yes

By issuing sbatch multidir.sh in the parent directory, all simulations are run concurrently using one full Mahti node without hyperthreading so that each system is allocated 16 cores. As the systems were initialized with different velocities, we obtain 8 distinct trajectories and an improved sampling of the phase space (see RMSD analysis below). This is a great option for enhanced sampling when your system does not scale beyond a certain core count.

For further details on running Gromacs multi-simulations, see the official Gromacs documentation.

Visualizing trajectories and graphs

In addition to view (not available at CSC, though) tool of Gromacs, trajectory files can be visualized with the following programs:

• PyMOL molecular modeling system (not available at CSC)
• VMD visualizing program for large biomolecular systems
• Grace plotting graphs produced with Gromacs tools

Note

Please don't run visualization or heavy Gromacs tool scripts in the login node (see usage policy for details). You can run the tools in the interactive partition by prepending your gmx_mpi command with orterun -n 1, e.g. orterun -n 1 gmx_mpi msd -n index -s topol -f traj).

References

Cite your work with the following references:

• GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. Hess, B., Kutzner, C., van der Spoel, D. and Lindahl, E. J. Chem. Theory Comput., 4, 435-447 (2008).
• GROMACS: Fast, Flexible and Free. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.Berendsen, J. Comp. Chem. 26 (2005) pp. 1701-1719
• GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. Lindahl SoftwareX 1 (2015) pp. 19-25
• Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl 8759 (2015) pp. 3-27
• GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl Bioinformatics 29 (2013) pp. 845-54

See your simulation log file for more detailed references for methods applied in your setup.

More information

• Gromacs home page: http://www.gromacs.org/
• Hands-on tutorials by Justin A. Lemkul, on GROMACS tutorial home and by Bert de Groot group
• Lots of material at BioExcel EU project
• HOW-TO section on the Gromacs pages
• Gromacs documentation and mdrun performance checklist
• The PRODRG Server for online creation of small molecule topology
• 2021 Advanced Gromacs Workshop materials

Last edited Tue May 3 2022