Restart MD run from a particular time moment in *.xtc file?

User discussions
1

Hello, dear GROMACS users & developers!

It happened that one of my GROMACS jobs was not finalised properly. As a result, I have the log, gro, edr, cpt, tpr files corresponding to the end of the simulation [ 1.5 ms ] , but the xtc file corresponds to an intermediate time moment [ 1 ms ] , from which the MD simulation job was extended. Apparently, the last 0.5 ms of the system trajectory is lost, and I need to restore it. Also, surprisingly, prev_cpt file seems to correspong to the time moment 1 ms.

I have two Qs :

  1. what is the reliable way to start the job from that intermediate time moment? shall I use prev_cpt as a restart point?

  2. what will GROMACS do with those log, gro, edr files, are they to be rewritten? Especially, I’m curious about the log file content, namely will GROMACS add new logs to the end of the file or will it rewrite the logs between 1 ms and 1.5 ms?

Thanks!