Gromacs is a software suite for high-performance molecular dynamics and output analysis.

Documentation

Gromacs home
Gromacs documentation home
Some tutorials...

Slurm scripts

Need to flesh this out...

#!/bin/bash
#SBATCH --time=1:00:00
#SBATCH --partition=norm
#SBATCH --ntasks=8
???

 

Build instructions for those who are curious

 

module load gcc/12.4.0
module load openmpi/5.0.5
module load cuda/12.0
rm -rf gromacs-2024.3/build
mkdir gromacs-2024.3/build
cd gromacs-2024.3/build
export OMPI_MCA_prte_silence_shared_fs=1
cmake -DCMAKE_INSTALL_PREFIX=/mnt/nasapps/production/gromacs/2024.3 \
    -DGMX_OPENMP=ON -DGMX_MPI=ON -DGMX_GPU=CUDA \
    -DCMAKE_BUILD_TYPE=Release -DGMX_DOUBLE=OFF \
    -DGMX_FFT_LIBRARY=fftw3 -DGMX_BUILD_OWN_FFTW=OFF \
    -DGMX_HWLOC=ON .. &&
make VERBOSE=1 -j 12 && make check && make install