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

[Vitaly V. Chaban]

trjconv -dump $last_frame -o conf.gro
grompp -c conf.gro

This will allow you to restart the simulation, if you do not care
about an exact continuation of the phase space trajectory that you
probably do not.






On Wed, Sep 2, 2015 at 10:51 AM, Adriana Garro <adrianagarrosl at gmail.com> wrote:
> 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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