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

[Chandan Choudhury]

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...”*