[gmx-developers] Inconsistent shifts. trjconv bug?

[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


>> 
>> 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
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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
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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
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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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