[gmx-users] Continuation of Serial MD simulation in Parallel

Mark Abraham mark.abraham at anu.edu.au
Mon Jul 3 15:10:31 CEST 2006

> Thanks so much for the answer.
> I have one more doubt. Could you please answer?
> I could make the change and run, but still the following line in the log
> file, "Starting time for run is 0 ps" (BLUE color), appears
> controversial to me.

If you use grompp to do the restart, your .mdp file has a parameter that
is setting the initial time to zero. If you want to use grompp thus, you
need to use a different .mdp for simulation restarts compared with your
restarts after equilibration. Using tpbconv for restarts doesn't have this
problem. Reading and understanding the relevant manual sections about what
each command in your .mdp file actually does, would also avoid this
problem, and probably dozens of others.

Why is it, I wonder to myself rhetorically, that every second reply I make
on here suggests somebody read the manual/man pages/web pages/original
literature??? :-)


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