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

[Johnny Lu]

http://www.gromacs.org/Documentation/How-tos/Doing_Restarts



On Tue, Sep 1, 2015 at 11:53 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> 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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>
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