GROMACS is a versatile package for performing molecular dynamics, for example, simulating the Newtonian equations of motion for systems with hundreds to millions of particles.

Work in Progress for Phase-2 Documentation

The content of this section is currently being updated to include material relevant for Phase-2 of Setonix and the use of GPUs.
On the other hand, all the existing material related to Phase-1 and the use of CPU compute nodes can be considered safe, valid and up-to-date.

It is primarily designed for biochemical molecules like proteins, lipids, and nucleic acids that have a lot of complicated bonded interactions. Because 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, for example, polymers.

Using GROMACS on Setonix

Gromacs is compiled with the GNU programming environment.

All GROMACS installations on Setonix have been patched with Plumed.

To use GROMACS, load the appropriate module:

$ module load gromacs/2021.4 

For most modules, both single-precision and double-precision versions of GROMACS have been installed.
Double-precision executables have the default suffix _d. For example, mdrun_mpi_d is compiled with MPI and double precision.

Example: Running GROMACS 

This is an example of a GROMACS job queueing script.

Listing 1. Example of a job queueing script using GROMACS Test Case A
#!/bin/bash --login
#SBATCH --nodes=1
#SBATCH --ntasks=128
#SBATCH --exclusive
#SBATCH --time=00:05:00
#SBATCH --account=[your-project]

module load gromacs/2021.4
srun -N 1 -n 128 gmx_mpi_d mdrun -s ion_channel.tpr -maxh 0.50 -resethway -noconfout -nsteps 10000 -g logile

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