On Fri, Oct 21, 2011 at 8:33 AM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > I try to restart my simulation - I have been able to continue the
> > simulation by restarting every 20 ns but after 80 ns I get a restart
> > file which gives me the following error when I try to run it again
>
> do your restart files contain ******* entries? In long simulations, this
> can happen if center of mass motion is not removed. The simulation still
> finishes normally and a rst file gets written, since internally, the
> coordinates are floats, but the fixed width format in the rst cant contain
> the numbers anymore.
>
This is especially common in explicit solvent simulations if you don't use
iwrap=1 (see previous posts on this list for more information). Even if you
remove COM motion (via nscm), your solvent naturally diffuses, and will
expand beyond the bounds of a fixed format restart file in terms of the size
of coordinates that can be expressed.
This should be fixed in the next release with the use of NetCDF restart
files.
>
> If that is the case, image your last good rst file and continue from
> there...
>
One thing you'll want to be careful of when you do this is to copy your
velocities over after you've done this, since ptraj (and cpptraj in
AmberTools 1.5, AFAIK) doesn't preserve these values, even if they exist.
HTH,
Jason
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Oct 21 2011 - 07:00:03 PDT
