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 topol.top -o em.tpr
gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
gmx energy -f npt.tpr -o density.xvg
gmx grompp -f nvt_mdrun.mdp -c npt.gro -p topol.top -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 topol.top -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.