[gmx-developers] Inconsistent shifts. trjconv bug?

[Berk Hess]

On 04/16/2012 12:20 PM, Erik Marklund wrote:
> 16 apr 2012 kl. 12.09 skrev 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
>
> Yes it does. I tried to find this issue, but failed. What is its id?
I think you problem probably has the same cause as:
http://redmine.gromacs.org/issues/809

Berk
>
> Best,
>
> Erik
>
>>>
>>>>
>>>> -----------------------------------------------
>>>> 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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>
> -----------------------------------------------
> 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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