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

Justin Lemkul jalemkul at vt.edu
Tue Sep 1 04:17:49 CEST 2015

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 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


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