Perhaps to clarify:
It appears that Bruno's problem is restarting a simulation, so a restart
file generated as Jason suggested (i.e. without velocities) won't help in
that case.
What Jason does implicitly mention, is that Bruno probably doesn't have a
problem, as long as he switches to iwrap=1 in the simulation. Even though
the coordinates extracted from it may look weird, they are probably ok in
the real periodic system.
As Bruno himself already mentioned, you can process the .mdcrd / restart
files later in ptraj to get coordinates that do look ok.
So, as long as your energies etc. look fine, you can just continue MD from
the restart file generated with iwrap=1.
--Marc
On 16 August 2011 12:16, Jason Swails <jason.swails.gmail.com> wrote:
> You can use cpptraj or ptraj to create restart files from the mdcrd:
>
> trajin my_traj.mdcrd 5 100 5
> trajout my_snapshots.restrt restart
>
> However, note that you will *not* have any velocity information, so it can
> never be a true restart. Therefore, you may be better off using the
> restart
> that has been working for you, but just looks weird.
>
> HTH,
> Jason
>
> On Mon, Aug 15, 2011 at 10:32 PM, Bruno Rodrigues <bbrodrigues.gmail.com
> >wrote:
>
> > Dear all,
> >
> > I'm running a long simulation of DNA and water, with 20 different inputs.
> > However, at the 19th, the simulation stopped, and did not restart.
> >
> > I searched on the list and found that, because I didn't use iwrap, maybe
> > there are some coordinates very far from the origin and sander didn't
> read
> > it.
> >
> > However, if I use iwrap, it messes out the DNA inside the box. I managed
> to
> > bring the molecules back to the box by centering them. But how can I
> > generate a restart file from the mdcrd ones?
> >
>
> > Regards,
> >
> > --
> > --
> > Bruno Barbosa Rodrigues
> > PhD Student - Physics Department
> > Universidade Federal de Minas Gerais - UFMG
> > Belo Horizonte - Brazil
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Aug 16 2011 - 04:30:05 PDT
