Continuing simulation after timeout

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GROMACS version: 2020.3
GROMACS modification: No
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I am attempting to continue a simulation from when it timed out. My simulation made it to production and has a step5_1_prev.cpt file. I am using a script from CHARMM-GUI and am having issues with modifying it. I thought about commenting out the minimization and equilibration steps first. Should I add the -cpi flag to each of the lines in my production script?

Please see the copied link for github repository. I tried pasting the code in this forum and the result was not pretty. Thank you!

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Yes, you should add the -cpi <filename> option to avoid overwriting what is already finished.

I would suggest commenting out the lines starting the steps that are finished, but as long as you provide checkpoint files it does not make much difference. You will get a new copy of the final configuration and lose the performance information in the log file if you run the finished jobs.