Running GROMACS with Spack and Slurm

GROMACS version: 2021.2
GROMACS modification: No

Hello, I am running GROMACS on a computing cluster using Slurm and the GROMACS spack package. I’m new to GROMACS, so I was provided with a basic simulation to test out, but I have run into an error that I haven’t been able to solve.

I was provided various files to start the simulation and these commands:

gmx genconf -f EC_LPG.gro -o EC_box_new.gro -nbox 6 6 6 -rot
gmx grompp -f minim.mdp -c EC_box_new.gro -p -o em.tpr
gmx grompp -f nvt.mdp -c em.gro -p -o nvt.tpr
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p -o npt.tpr
gmx energy -f npt.tpr -o density.xvg
gmx grompp -f nvt_mdrun.mdp -c npt.gro -p -o mdrun.tpr

I modified the commands slightly (srun gmx_mpi…) to work with slurm and spack. However, when the person who provided me the files runs this simulation (on a different computing cluster, not using spack), the step “gmx grompp -f nvt.mdp -c em.gro -p -o nvt.tpr” also generates other files, such as the nvt.gro and nvt.cpt necessary for the next step. However, when I run the same step, these files do not show up in my directory.

I considered using an additional step, such as “convert-trj” to convert the nvt.tpr file to nvt.gro, but this doesn’t work to create the nvt.cpt file.

Any advice would be greatly appreciated.

gmx mdrun generates energy file (edr), checkpoint file (.cpt), trajectory file (*xtc/trr) and final structure file *.gro given a tpr file (not gmx grompp). This seems missing in your command list.