What is the exact command to run a (CHARMM-GUI) step6.1_equilibration.cpt Checkpoint File?

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1

GROMACS version: 2025.3
GROMACS modification: Yes/No
Here post your question:

Hello I had originally generated a step6.1_equilibration.mdp via CHARMM-GUI where a subsequently generated step6.1_equilibration.cpt was generated via running out of time.

Accordingly, being a CHARMM-GUI File, would be the exact gmx command using this Checkpoint File considering the CHARMM-GUI nature be the below (I could not discover this confirmation within this Forum):

gmx mdrun -v -deffnm step6.1_equilibration -cpi step6.1_equilibration.cpt

Thanks if you can confirm since I would need the Slurm Admin. to modify the .sh Script so want to manage his time:).

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Yes that should be the correct command. Note that CHARMM-GUI has nothing to do with this as it’s a file generated periodically during mdrun, it just depends on how the file is named. The default checkpoint file name is state.cpt but since you use the -deffnm option it is overwritten.

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Hello lmullender ok thank you for your kind update:)