[gmx-users] extend a simulation just with xtc file

[Adriana Garro]

Hi
No, I don't have a cpt file, I mean I have one but it is the final cpt
because the simulation finished (in a wrong way). The problem came up in
the last 15 ns, I had checked before and it was going fine.  I already
reran the simulation but this time using subtrajectories.
Thanks!

Adriana

***********************************************************
Dra. Adriana D. Garro
Química Medicinal
Facultad de Química, Bioquímica y Farmacia
Universidad Nacional de San Luis
IMASL-CONICET
San Luis, Argentina

Tel..............:+54 266 4424689  int 6153
e-mail...: adgarro at unsl.edu.ar
e-mail...:  adrianagarrosl at gmail.com


**********************************************************

2015-09-02 0:53 GMT-03:00 Johnny Lu <johnny.lu128 at gmail.com>:

> the position in xtc is not accurate enough for restarting simulation. xtc
> has no velocity.
>
> restart need position, velocity, and variables for the thermostat and
> barostat.
>
> Do you have any cpt file? may be you can run a restart using cpt and tpr
> files.
>
> On Mon, Aug 31, 2015 at 10:21 PM, Adriana Garro <adrianagarrosl at gmail.com>
> wrote:
>
> > :-(  ok
> > Thanks, I will have to run this simulation again.
> > Bye
> >
> > Adriana
> >
> > ***********************************************************
> > Dra. Adriana D. Garro
> > Química Medicinal
> > Facultad de Química, Bioquímica y Farmacia
> > Universidad Nacional de San Luis
> > IMASL-CONICET
> > San Luis, Argentina
> >
> > Tel..............:+54 266 4424689 int 6153
> > e-mail...: adgarro at unsl.edu.ar
> > e-mail...:  adrianagarrosl at gmail.com
> >
> >
> > **********************************************************
> >
> > 2015-08-31 23:17 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:
> >
> > >
> > >
> > > On 8/31/15 11:52 AM, Adriana Garro wrote:
> > >
> > >> Dear Gromacs users,
> > >>
> > >> My 100 ns simulation finish but in a wrong way, I knew it when I tried
> > to
> > >> use an analizing tool and the message was the next one
> > >>
> > >> Fatal error:
> > >> Magic Number Error in XTC file (read 0, should be 1995)
> > >>
> > >> It seems that this kind of error is  related to the network file
> system.
> > >> My first attempt was restart (I am using gromacs 4.5.5)
> > >> mdrun -s topol.tpr -cpi state.cpt
> > >> but of course it finished immediately then I realized that the number
> of
> > >> steps was reached.
> > >>
> > >> I did a copy of the md.xtc file  while it was running in order to see
> > how
> > >> things were going on, aproximately at 85 ns, so I would like to know
> if
> > it
> > >> is possible to extend my simulation using this 85ns xtc file. (without
> > >> having cpt file)
> > >>
> > >>
> > > The .xtc has nothing useful about the state of the simulation.  A set
> of
> > > coordinates is inadequate for properly continuing a simulation.
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==================================================
> > > --
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