[gmx-developers] Inconsistent shifts. trjconv bug?

[Berk Hess]

On 04/16/2012 12:07 PM, Erik Marklund wrote:
>
> 16 apr 2012 kl. 11.32 skrev Erik Marklund:
>
>> Hi,
>>
>> I have a few trajectories from simulations of solvated proteins and 
>> DNA that causes problems when I pass them through trjconv. Here's the 
>> command line:
>>
>> trjconv  -f run.xtc -s run.tpr -o tst.xtc -pbc mol
>>
>> Choosing group "Protein" for output, I get heaps of inconsistent shits:
>>
>> "...
>> There were 1 inconsistent shifts. Check your topology00 time 4000.000
>> There were 1 inconsistent shifts. Check your topology
>> ..."
>>
>> These trajectories were saved frequently, some every 10 ps. If I use 
>> -dt 1000 the errors disappear, probably because I skip certain 
>> problematic frames. No problems were reported in the logfiles from 
>> the simulations and this problem appears in braches release-4-6 and 
>> release-4-5-patches, and the official 4.5.5 release. The simulations 
>> were all done with release-4-5-patches.
>>
>> To me this looks like a bug.
>
>
> I gess my qustion is: should I file a redmine?
Does you xtc file contain a non-contiguous subset of the system?
In that case your issue is probably already filed.

Cheers,

Berk
>
>>
>> -----------------------------------------------
>> Erik Marklund, PhD
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,    75124 Uppsala, Sweden
>> phone:    +46 18 471 6688        fax: +46 18 511 755
>> erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>
>> http://www2.icm.uu.se/molbio/elflab/index.html
>>
>> --
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>
> -----------------------------------------------
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 6688        fax: +46 18 511 755
> erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>
> http://www2.icm.uu.se/molbio/elflab/index.html
>
>
>

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