[gmx-developers] Inconsistent shifts. trjconv bug?

Tsjerk Wassenaar tsjerkw at gmail.com
Tue May 29 13:31:01 CEST 2012 

Hi Erik,

Probably because g_bundle tries removing pbc for the whole system
prior to doing analysis on part of it.

Cheers,

Tsjerk

On Tue, May 29, 2012 at 1:20 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> 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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>
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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
>
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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
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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

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