[gmx-developers] Inconsistent shifts. trjconv bug?

[Erik Marklund]

16 apr 2012 kl. 13.55 skrev Erik Marklund:

> 
> 16 apr 2012 kl. 13.26 skrev 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
> 
> Thanks. That may be related. I tried, however, to make a new tpr file of the subsystem with tpbconv, which led to other problems with trjconv:
> 
> -------------------------------------------------------
> Program trjconv, VERSION 4.6-dev-20120412-24879-dirty-unknown
> Source code file: /home/erikm/source/GMX/gmx_gerrit/gromacs/src/gmxlib/mtop_util.c, line: 747
> 
> Software inconsistency error:
> Position restraint coordinates are missing
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> 
> In this particular case I had applied position restraints to parts of system. I think this calls for a redmine issue for tpbconv.
> 
> Best,
> 
> Erik

Hi again.

This problem is consistently reoccurring when I'm now simulating a protein interacting with a periodic DNA structure. I get these inconsistent shifts when analyzing my trajectories even if I use the trr file as input, also when choosing to process the entire system with e.g. trjconv. This suggests to me that redmine issue 809 is not the source of the problem. I've tried the release-4-6 branch too for analysis, but it doesn't help.

I'll make a redmine isssue of it thi afternoon unless someone points out what I might be overlooking.

Best,

Erik

> 
> 
>>> 
>>> 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
>>>>>> 
>>>>>> --
>>>>>> gmx-developers mailing list
>>>>>> gmx-developers at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>>> Please don't post (un)subscribe requests to the list. Use the
>>>>>> www interface or send it to gmx-developers-request at gromacs.org.
>>>>> 
>>>>> -----------------------------------------------
>>>>> 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
>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> -- 
>>>> gmx-developers mailing list
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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
> 
> -- 
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
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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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