[gmx-users] gmxcheck : Magic Number Error in XTC file (read 0, should be 1995)

[Amit Kumawat]

Thanks a lot chandan.

Regards,
Amit R. Kumawat
Junior Research Fellow,
C/O Dr. Suman Chakrabarty
Physical & Materials Chemistry Division
CSIR-National Chemical Laboratory
Pune, India - 411008
Mobile 09579195769


On Thu, Dec 25, 2014 at 4:54 PM, Chandan Choudhury <iitdckc at gmail.com>
wrote:

> Dear Amit,
>
> I do not have the solution of this problem. I have also encountered the
> similar error.
> What I do to avoid such thing, is (a) I run simulation in steps of shorter
> time (say 50 ns).
> (b) Then continue the simulation for larger times using the cpt file (
> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations).
> I do keep a backup of the cpt files.
> In this way, whenever I find the corruption in the trajectory. I do have
> cpt file from the earlier runs,
> which I can use to extend.
>
> Hope this would help you!
>
> Chandan
>
> On Thu, Dec 25, 2014 at 3:30 PM, Amit Kumawat <amit.kumawat20 at gmail.com>
> wrote:
>
> > Thank you very much David. Out of the complete trajectory I identified
> all
> > those frames which are corrupted and manually concatenated the rest of
> the
> > trajectory. Can you provide me suggestion for the possible source of
> error.
> > Because in the log file I could not see any out of disk space error and I
> > have been using the same version of gromacs  for initiating or extending
> > the simulation
> >
> > Regards,
> > Amit R. Kumawat
> > Junior Research Fellow,
> > C/O Dr. Suman Chakrabarty
> > Physical & Materials Chemistry Division
> > CSIR-National Chemical Laboratory
> > Pune, India - 411008
> > Mobile 09579195769
> >
> >
> > On Wed, Dec 24, 2014 at 8:56 PM, David van der Spoel <
> spoel at xray.bmc.uu.se
> > >
> > wrote:
> >
> > > On 2014-12-24 15:33, Amit Kumawat wrote:
> > >
> > >> Dear Gromacs Users,
> > >>
> > >> I have a trajectory of 2microsecond.
> > >> I am trying to use gmxcheck to analyse trajectory but I am getting
> > >> following error;
> > >>
> > >> Program gmxcheck, VERSION 4.6.5
> > >> Source code file:
> /home/suman/sources/gromacs-4.6.5/src/gmxlib/xtcio.c,
> > >> line: 92
> > >>
> > >> Fatal error:
> > >> Magic Number Error in XTC file (read 0, should be 1995)
> > >>
> > >> I have seen similar questions in the mailing list describing the
> > >> trajectory
> > >> may be corrupted. If its true in all the cases of this error, Is there
> > any
> > >> way to recover the trajectory?
> > >>
> > >> Please provide suggestion to solve the error.
> > >>
> > > start with
> > > trjconv -f old.xtc -o new.xtc
> > > to see how much is corrupt.
> > >
> > >
> > >
> > >> Regards,
> > >> ​Amit
> > >>
> > >> =============================​
> > >>
> > >> Amit R. Kumawat
> > >> Junior Research Fellow,
> > >> Physical & Materials Chemistry Division
> > >> CSIR-National Chemical Laboratory
> > >> ​Pune, INDIA​
> > >>
> > >> ​=============================​
> > >>
> > >>
> > >
> > > --
> > > David van der Spoel, Ph.D., Professor of Biology
> > > Dept. of Cell & Molec. Biol., Uppsala University.
> > > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> > > spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> > > --
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>
> --
>
> --
> Chandan Kumar Choudhury
> National Chemical Laboratory, Pune
> India
>
> *"All work and no play makes Jack a dull boy...”*
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