GROMACS version: 2025.3
GROMACS modification: Yes/No
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Hello Gromacs Forum, I need to re-execute a gromacs nvt run with a newly generated checkpoint file and understand that within iTerm the command would be:
gmx mdrun -v -deffnm step6.1_equilibration -cpi step6.1_equilibration.cpt
However, I will be executing this command within the NSF Slurm via the command:
sbatch Gromacs_7dwb_OPM_run.sh
where Gromacs_7dwb_OPM_run.sh will call:
bash_gromacs.sh exhibited in the attached screenshots labeled 1-3
Accordingly if someone could recommend the best way to edit the above. I see three steps where mdrun is called, and I’m not sure which of them (one or all) should be modified with the Checkpoint Command. The three lines are in the respective sections of the Minimization, Equilibration, and Production steps of this bash_gromacs.sh script. It could be that i´de have to take out some of the earlier steps, but im not savvy enough towards properly editing the above. Any help would be appreciated, thanks:)