[gmx-users] Continuing a simulation

Ankita naithani ankitanaithani at gmail.com
Mon Dec 24 17:35:20 CET 2012


I am running a protein simulation for 70 ns. I had a MPI run but due
to my time constraints on the server, it stopped after 28ns. Now, I
want to continue the simulation from the same point  up until I use up
my server time.

I just wanted to confirm that there are two checkpoint files written,
md.cpt and md_prev.cpt. It would be really helpful if anyone could
advice as to which file would be better to choose to continue the

Also, I wanted a confirmation that if I use:

mdrun -s topol.tpr -cpi md.cpt -append

Do I also need to add -deffnm md?

and if I run mdrun, would it then continue from say 28ns and up until
the time specified in the .mdp file? The reason I wanted to confirm
this is that before submitting it to the server, I ran it in my local
machine and when I see the log file, it shows step 0 and Time 0.0000,
does that mean it is starting the simulation from scratch because I
had expected it to show me step from wherever it exited last and
continue from there on.

Would really appreciate if anyone could guide me further.

Ankita Naithani

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