[gmx-developers] Inconsistent shifts. trjconv bug?

Erik Marklund erikm at xray.bmc.uu.se
Tue May 29 13:20:08 CEST 2012 

Hi,

Thanks. That's a good point. I'll investigate this further before filing an issue. Still, the error pops up in e.g. g_bundle when analyzing only non-periodic parts of the system.

Erik


29 maj 2012 kl. 13.08 skrev Tsjerk Wassenaar:

> Hey Erik,
> 
> Aren't you asking for trouble using -pbc mol with infinite molecules?
> To get a nice visualization, you would probably have to split the
> trajectory in a protein one, a DNA one and a solvent one, which you
> process separately and combine again later. Mind not to do fitting...
> Or hack trjconv so it applies pbc options only to a selection of
> atoms, apart from the output group.
> 
> Cheers,
> 
> Tsjerk
> 
> On Tue, May 29, 2012 at 12:44 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
>> 
>> 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
>> 
>> --
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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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>> 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
>> gmx-developers at gromacs.org
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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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> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> 
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> 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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