[gmx-users] Magic number error in XTC file

[GAYATHRI S]

Hi Tsjerk,

Thank you for your help. I tried what you had asked me to do:

$trjconv -f production_1.trr -o production_1.xtc -n index.ndx

Then, I selected the entire system from the index file.

However, when I used gmxcheck to verify the output file production_1.xtc,
I got the following error:

Fatal error:
No XTC!

Please suggest how to resolve this issue.

Thank you.

Regards,
Gayathri

> 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.
> --
> Gromacs Users mailing list
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