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

[Johnny Lu]

can extend simulation if the number of steps were reached.
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

That said, does extending the simulation avoid the problems that you found
in the simulation?

On Tue, Sep 1, 2015 at 11:54 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> 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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>>
>>
>