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?
Thankyou
Hi,
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…
Thank you for your guidance.