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
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Tue Aug 16 2011 - 05:00:03 PDT
