[gmx-users] Magic number error in XTC file

[Tsjerk Wassenaar]

Hi Gayathri,

For the XTC file you used only a selection of atoms to write out. The TRR
file always contains everything. With the conversion from TRR to XTC make
sure to write the same selection as is in the other XTC files.

Hope it helps,

Tsjerk

On Thu, Jul 28, 2016 at 7:36 AM, GAYATHRI S <gayathri.s at iitb.ac.in> wrote:

> Dear all,
>
> I had a run an MD simulation (GROMACS 4.6.6) which was abruptly stopped
> due to power failure. Then, I extended the simulation using the commands:
>
> $tpbconv -s production.tpr -o production_2.tpr -untill 50000
>
> $mdrun -v -s production_2.tpr -deffnm production_2 -cpi production.cpt
>
> Then, when the simulation was complete, I renamed the output files of the
> first simulation as production_1. Next, I wanted to merge the trajectories
> of both the runs; hence, I used the following command:
>
> $trjcat -f production_1.xtc production_2.xtc -o production.xtc -overwrite
>
> Fatal Error: Magic number error in XTC file
>
> When I went through the mailing list archive, I found that this error is
> shown when the trajectory is corrupted.
> So, I used gmxcheck to find out which of the trajectories were corrupted.
> I discovered that production_1.trr did not show any error, but
> production_1.xtc showed the same error.
> Hence, I used trjconv to make a new production_1.xtc
>
> $trjconv -f production_1.trr -o production_1.xtc
>
> Again, I checked the new file for error using gmxcheck. When everything
> looked good, I tried the trjcat command again, only to get the following
> error
>
> Fatal error: Different numbers of atoms (584885/9944) in the files.
>
> Please suggest how to resolve the issue.
>
> Thank you.
>
> Regards,
> Gayathri.
>
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-- 
Tsjerk A. Wassenaar, Ph.D.