Hi,
If a restart file is corrupted, unfortunately your only recourse is to
restart your simulation from the last good restart file. You can check
if your restart is really corrupted by trying to open it with cpptraj
or with the visualization program of your choice (e.g. VMD).
There are two things you can try to avoid this in the future. One is
to use coordinate imaging (iwrap=1) to prevent your molecules from
diffusing too far. The second is to use NetCDF restarts (ntxo=2),
which are written with higher precision than ASCII restarts.
Hope this helps,
-Dan
On Fri, Feb 13, 2015 at 11:03 AM, Edward Kalkreuter <rekalkre.ncsu.edu> wrote:
> Hi,
>
> I am running a simulation with Sander on Amber 14, and everything was
> working fine until I tried to go from 60ns to 65ns. When I tried to proceed
> from 65ns to 70ns, I received a message on the output file that said:
>
> I could not understand line 25860
> -49.2682148 -462.2942377 -327.7409275
>
> I realize that this is an error in the previous restart file, but I am not
> sure how I can fix this. I read through the Amber 14 forums and could not
> understand how to fix this even though I know I'm not the first one to get
> this type of error. I'm relatively new, so I'm hoping this is a simple fix.
>
> Thank you
>
> --
> Edward Kalkreuter
> PhD Candidate, Williams Lab
> Department of Chemistry
> North Carolina State University
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Feb 13 2015 - 13:00:03 PST
