...

• 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.

...

In order to load the GPU enabled version:

Coming soon...

Submission

...

script examples

Simple 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 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

coming soon...

Related Modules

...

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.

Usage tips

System preparation

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.

...

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

References

1. GROMACS User-Guide
2. PLUMED Home