Gmx command line was not found in slurm_script HPC cluster

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Hi gromacs users,
Im running mdrun in HPC cluster, here is my sbatch scripts
#!/bin/bash
#SBATCH --job-name=coumaric-acid
#SBATCH --time=24:00:00
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=4096
#SBATCH --cpus-per-task=1
module load gromacs/5.1.4
gmx mdrun -deffnm md_100

but it failed, when checking the issue, it say that gmx command line was not found.
Any advices for this, thank you in advance

2

Hi Truong,

maybe the GROMACS executable is not called gmx in your case. Try to find out what the module does (it should add the GROMACS bin path to your $PATH environment variable), then look in that directory how the executables are called. Could simply be mdrun instead of gmx. By the way, have you considered using a more recent GROMACS version? 5.1.4. is quite old already :)

Best,
Carsten