Continuing simulation with cpt file after a crash

GROMACS modification: No

Can we continue a simulation using -cpi .cpt file after it has written a series of step.pdb files and crashed in previous step (after ~800 ns)?
Can I simply resubmit the mdrun command with cpt file and tpr used previously?

In In the xtc where it stopped the simulation, I see some atoms have moved out of the box (after pbc treatment) and molecules appear broken ?
What can I do?



I believe you most ceirtainly can, just by adding -cpi state.cpt in the mdrun command options.

It’s unlikely the issue is going to disappear by itself, though; I usually get this kind of output when starting from a very ‘non-equilibrated’ configuration (e.g. upon doing steepest descend or some other energy minimization, before the actual equilibration run), so I guess something very wrong is going on. However, after 800 nanoseconds it seems unlikely the crash is caused by the initial configuration not being properly minimized…

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Thank you for your guidance.