On Fri, Oct 21, 2011 at 9:59 AM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> great - so adding iwrap=1 will solve it for future simulation as I
> understand(?)
Yes.
> but for long simulations you will have to image center
> once in a while?
>
No. iwrap=1 does that automatically before writing trajectory snapshots and
restart files.
HTH,
Jason
>
>
> On Fri, Oct 21, 2011 at 3:37 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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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 - 08:00:02 PDT
