Bruno, the question is: do you have ****** instead of a floating point in
the restart file that didn't work?
If so, the coordinate value probably exceeded 1000 (or actually
999.9999999), the maximum possible in the .rst format, and would be the
reason AMBER can't read it and continue simulation with it. That's the
reason to use iwrap=1.
I'm not entirely sure if you tried re-running the step that created the
problematic .rst file with iwrap=1 or not.
Apart from whether coordinates in output files are imaged or not, I don't
think there is a difference in running with iwrap=1 or iwrap=0 in
sander/pmemd (although I could be wrong...). This means that there probably
won't be a problem in switching to iwrap=1 in the step that generated the
problematic .rst file.
--Marc
On 16 August 2011 12:40, Bruno Rodrigues <bbrodrigues.gmail.com> wrote:
> Well,
>
> Maybe I did not properly explian my problem:
>
> I realized that with iwrap=1 the DNA shifts to the border of the box, and
> sometimes breaks the two strands apart. I reported the problem before at
> the
> list, but didn't get any clue.
>
> So I decided to switch iwrap off. As the simulation lasts for 40ns with a
> T-jump from 300 up to 400K, I *guess* the problem is related with molecules
> very far from the solute. I read something about it on the developer's
> list.
> I know these molecules far from the solute are not a true problem, as I can
> always bring them back to the 1st box with ptraj.
>
> So here is the puzzle:
>
> I have the coordinate and restart files from the last simulation. The
> restart generated does not work for the next step. The output complains
> that
> can not read the file. Then, I re-imaged the mdcrd files back to the first
> cell. I would like to generate a restart file from the last frame of *this*
> mdcrd, as the molecules look fine in the first cell.
>
> But as you mentioned, there's no velocity information. Should I equilibrate
> it for longer before continue with the heating? What can I do to avoid it?
> And did someone else have problems with iwrap?
>
> Thank you in advance.
>
> On Tue, Aug 16, 2011 at 8:26 AM, Marc van der Kamp <
> marcvanderkamp.gmail.com
> > wrote:
>
> > 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
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> --
> 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
>
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Received on Tue Aug 16 2011 - 05:00:03 PDT
