<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>16 apr 2012 kl. 13.26 skrev Berk Hess:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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On 04/16/2012 12:20 PM, Erik Marklund wrote:
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<div>16 apr 2012 kl. 12.09 skrev Berk Hess:</div>
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<div bgcolor="#FFFFFF" text="#000000"> On 04/16/2012 12:07 PM,
Erik Marklund wrote:
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<div>16 apr 2012 kl. 11.32 skrev Erik Marklund:</div>
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<div>Hi,<br>
<br>
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:<br>
<br>
trjconv -f run.xtc -s run.tpr -o tst.xtc -pbc mol<br>
<br>
Choosing group "Protein" for output, I get heaps of
inconsistent shits:<br>
<br>
"...<br>
There were 1 inconsistent shifts. Check your
topology00 time 4000.000 <br>
There were 1 inconsistent shifts. Check your
topology<br>
..."<br>
<br>
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.<br>
<br>
To me this looks like a bug.<br>
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I gess my qustion is: should I file a redmine?</div>
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Does you xtc file contain a non-contiguous subset of the
system?<br>
In that case your issue is probably already filed.<br>
<br>
Cheers,<br>
<br>
Berk<br>
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<div>Yes it does. I tried to find this issue, but failed. What
is its id?</div>
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I think you problem probably has the same cause as:<br>
<a class="moz-txt-link-freetext" href="http://redmine.gromacs.org/issues/809">http://redmine.gromacs.org/issues/809</a><br>
<br>
Berk<br></div></blockquote><div><br></div><div>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:</div><div><br></div><div><div>-------------------------------------------------------</div><div>Program trjconv, VERSION 4.6-dev-20120412-24879-dirty-unknown</div><div>Source code file: /home/erikm/source/GMX/gmx_gerrit/gromacs/src/gmxlib/mtop_util.c, line: 747</div><div><br></div><div>Software inconsistency error:</div><div>Position restraint coordinates are missing</div><div>For more information and tips for troubleshooting, please check the GROMACS</div><div>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></div><div>-------------------------------------------------------</div><div><br></div><div>In this particular case I had applied position restraints to parts of system. I think this calls for a redmine issue for tpbconv.</div><div><br></div><div>Best,</div><div><br></div><div>Erik</div></div><div><br></div><br><blockquote type="cite"><div bgcolor="#FFFFFF" text="#000000">
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<div>Best,</div>
<div><br>
</div>
<div>Erik</div>
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-----------------------------------------------<br>
Erik Marklund, PhD<br>
Dept. of Cell and Molecular Biology, Uppsala
University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: +46 18 471 6688 fax: +46 18 511 755<br>
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<div>Dept. of Cell and Molecular Biology,
Uppsala University.</div>
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Sweden</div>
<div>phone: +46 18 471 6688 fax: +46
18 511 755</div>
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<div>-----------------------------------------------</div>
<div>Erik Marklund, PhD</div>
<div>Dept. of Cell and Molecular Biology, Uppsala
University.</div>
<div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div>
<div>phone: +46 18 471 6688 fax: +46 18 511
755</div>
<div><a moz-do-not-send="true" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div>
<div><a moz-do-not-send="true" href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div>
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