[gmx-users] restart md from the point it had stopped

[Tsjerk Wassenaar]

Hi Diego,

gmxcheck will tell you whether the last frame is corrupted (incomplete) or
not.
Besides, why do you write velocities and forces every 10 ps? Do you have to
much space on your hard-disk or do you need the velocities? Usually, writing
to the .trr will be a compromise between the amount of disk space you have
and the time you'll loose when restarting. I usually write one or two frames
to the .trr per day.

Cheers,

Tsjerk

On 10/8/07, Diego Enry <diego.enry at gmail.com> wrote:
>
> gmxcheck -f broken.trr
>
> check this information:
>
> Item        #frames Timestep (ps)
> Step           101    10
> Time           101    10
> Lambda        101    10
> Coords         101    10
> Velocities     101  10
> Forces           101  10
> Box            101    10
>
> I writing it every 1ps.
> I recommend you NOT to use the LAST frame because it may be corrupted
> if your simulation was terminated while writing this frame. To
> continue, specify the frame just before the last one find above.
>
> tpbconv -s broken.tpr -f broken.trr -e broken.edr -o continue.tpr -time 9
>
> Check If you write velocities&force to the .trr file, I think you
> can't get a good continuation without that information.
>
>
> On 10/8/07, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> > Hi Sarbani,
> >
> > Use tpbconv. You can only (properly) restart from a point where you have
> a
> > frame with velocities (in the .trr file) and preferrably energies
> (.edr).
> >
> > Best,
> >
> > Tsjerk
> >
> >
> >  On 8 Oct 2007 12:34:23 -0000, sarbani chattopadhyay
> > <sarbani_c84 at rediffmail.com> wrote:
> > >
> > >
> > >
> > >
> > > hi,
> > >   I have been running a molecular dynamics simulation for 2
> > nanoseconds.But it stopped in
> > > the middle because of an internal problem.Is there any way to restart
> the
> > simulation from
> > > the point it has stopped?
> > >
> >        Thank all
> > >
> >          Sarbani
> > >
> > >
> > > _______________________________________________
> > > gmx-users mailing list    gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before
> posting!
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read
> > http://www.gromacs.org/mailing_lists/users.php
> > >
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> >  P: +31-30-2539931
> > F: +31-30-2537623
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read
> > http://www.gromacs.org/mailing_lists/users.php
> >
>
>
> --
> Diego Enry B. Gomes
> Laboratório de Modelagem e Dinamica Molecular
> Universidade Federal do Rio de Janeiro - Brasil.
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071009/4a69d2e3/attachment.html>