<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. 13.55 skrev Erik Marklund:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div 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></div></blockquote><div><br></div>Hi again.</div><div><br></div><div>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.</div><div><br></div><div>I'll make a redmine isssue of it thi afternoon unless someone points out what I might be overlooking.</div><div><br></div><div>Best,</div><div><br></div><div>Erik</div><div><br><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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>-----------------------------------------------</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>
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