[gmx-users] Continuing a simulation

[Mark Abraham]

Check out http://www.gromacs.org/Documentation/How-tos/Doing_Restarts

On Mon, Dec 24, 2012 at 5:35 PM, Ankita naithani
<ankitanaithani at gmail.com>wrote:

> Hi,
>
> 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
> simulation?
>

Per the above, use gmxcheck and choose for yourself :-)


> 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?
>

Don't know, depends in part on the behaviour you want to see... Backing up
your files and trying it to see is much more efficient than emailing the
list :-)

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.
>

That means the restart didn't work, but without looking at the .log file
and knowing the command line and contents of the files, nobody can know
why. The restart can only start from the configuration in the .cpt or the
.tpr, and in general neither of those will be at the point the crash
occurred.

Mark