[gmx-developers] Inconsistent shifts. trjconv bug?

[Erik Marklund]

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?

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
>>> 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
>> 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
http://www2.icm.uu.se/molbio/elflab/index.html

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