How to run gromacs on HPC?

User discussions
1

Dear gromacs users:

I would like to use the cluster to run my simulations. Indeed this is the first time I am using cluster. I have prepared the md.tpr file but don’t know how to run the mdrun command. This is the command which is used for LAMMPS on the same cluster. How should I change it for Gromacs?

srun --propagate=NONE -p parallel -n 30 /lustre/home/frusciano/lammps-17Apr2024/src/lmp_mpi -in input_file_name  &>SC.out &

I changed this command to:

srun --propagate=NONE -p parallel -n 30 /nfsexports/SOFTWARE/gromacs-2024.3/build/bin/gmx_mpi -in mdrun -deffnm nvt5 &>SC.out &

but, It doesn’t work

Thanks

2

I guess
srun --propagate=NONE -p parallel -n 30 /nfsexports/SOFTWARE/gromacs-2024.3/build/bin/gmx_mpi mdrun -deffnm nvt5 &>SC.out &
will work. However, even better would be to either use the module system on the cluster (module load gromacs/2024.3), if there is one, or do
source /nfsexports/SOFTWARE/gromacs-2024.3/build/bin/GMXRC
and (in either of those two cases) then
srun --propagate=NONE -p parallel -n 30 gmx_mpi mdrun -deffnm nvt5 &>SC.out &

3

Deat MagnusL,

Thanks a lot for your reply. I will check it