<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>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.</div><div><br></div><div>Erik</div><div><br></div><div><br><div><div>29 maj 2012 kl. 13.08 skrev Tsjerk Wassenaar:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hey Erik,<br><br>Aren't you asking for trouble using -pbc mol with infinite molecules?<br>To get a nice visualization, you would probably have to split the<br>trajectory in a protein one, a DNA one and a solvent one, which you<br>process separately and combine again later. Mind not to do fitting...<br>Or hack trjconv so it applies pbc options only to a selection of<br>atoms, apart from the output group.<br><br>Cheers,<br><br>Tsjerk<br><br>On Tue, May 29, 2012 at 12:44 PM, Erik Marklund <<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>> wrote:<br><blockquote type="cite"><br></blockquote><blockquote type="cite">16 apr 2012 kl. 13.55 skrev Erik Marklund:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">16 apr 2012 kl. 13.26 skrev Berk Hess:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On 04/16/2012 12:20 PM, Erik Marklund wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">16 apr 2012 kl. 12.09 skrev Berk Hess:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On 04/16/2012 12:07 PM, Erik Marklund wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">16 apr 2012 kl. 11.32 skrev Erik Marklund:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I have a few trajectories from simulations of solvated proteins and DNA that<br></blockquote><blockquote type="cite">causes problems when I pass them through trjconv. Here's the command line:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">trjconv -f run.xtc -s run.tpr -o tst.xtc -pbc mol<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Choosing group "Protein" for output, I get heaps of inconsistent shits:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">"...<br></blockquote><blockquote type="cite">There were 1 inconsistent shifts. Check your topology00 time 4000.000<br></blockquote><blockquote type="cite">There were 1 inconsistent shifts. Check your topology<br></blockquote><blockquote type="cite">..."<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">These trajectories were saved frequently, some every 10 ps. If I use -dt<br></blockquote><blockquote type="cite">1000 the errors disappear, probably because I skip certain problematic<br></blockquote><blockquote type="cite">frames. No problems were reported in the logfiles from the simulations and<br></blockquote><blockquote type="cite">this problem appears in braches release-4-6 and release-4-5-patches, and the<br></blockquote><blockquote type="cite">official 4.5.5 release. The simulations were all done with<br></blockquote><blockquote type="cite">release-4-5-patches.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">To me this looks like a bug.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I gess my qustion is: should I file a redmine?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Does you xtc file contain a non-contiguous subset of the system?<br></blockquote><blockquote type="cite">In that case your issue is probably already filed.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Cheers,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Berk<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Yes it does. I tried to find this issue, but failed. What is its id?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I think you problem probably has the same cause as:<br></blockquote><blockquote type="cite"><a href="http://redmine.gromacs.org/issues/809">http://redmine.gromacs.org/issues/809</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Berk<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks. That may be related. I tried, however, to make a new tpr file of the<br></blockquote><blockquote type="cite">subsystem with tpbconv, which led to other problems with trjconv:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-------------------------------------------------------<br></blockquote><blockquote type="cite">Program trjconv, VERSION 4.6-dev-20120412-24879-dirty-unknown<br></blockquote><blockquote type="cite">Source code file:<br></blockquote><blockquote type="cite">/home/erikm/source/GMX/gmx_gerrit/gromacs/src/gmxlib/mtop_util.c, line: 747<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Software inconsistency error:<br></blockquote><blockquote type="cite">Position restraint coordinates are missing<br></blockquote><blockquote type="cite">For more information and tips for troubleshooting, please check the GROMACS<br></blockquote><blockquote type="cite">website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br></blockquote><blockquote type="cite">-------------------------------------------------------<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">In this particular case I had applied position restraints to parts of<br></blockquote><blockquote type="cite">system. I think this calls for a redmine issue for tpbconv.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Best,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Erik<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi again.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">This problem is consistently reoccurring when I'm now simulating a protein<br></blockquote><blockquote type="cite">interacting with a periodic DNA structure. I get these inconsistent shifts<br></blockquote><blockquote type="cite">when analyzing my trajectories even if I use the trr file as input, also<br></blockquote><blockquote type="cite">when choosing to process the entire system with e.g. trjconv. This suggests<br></blockquote><blockquote type="cite">to me that redmine issue 809 is not the source of the problem. I've tried<br></blockquote><blockquote type="cite">the release-4-6 branch too for analysis, but it doesn't help.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I'll make a redmine isssue of it thi afternoon unless someone points out<br></blockquote><blockquote type="cite">what I might be overlooking.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Best,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Erik<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Best,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Erik<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-----------------------------------------------<br></blockquote><blockquote type="cite">Erik Marklund, PhD<br></blockquote><blockquote type="cite">Dept. of Cell and Molecular Biology, Uppsala University.<br></blockquote><blockquote type="cite">Husargatan 3, Box 596, 75124 Uppsala, Sweden<br></blockquote><blockquote type="cite">phone: +46 18 471 6688 fax: +46 18 511 755<br></blockquote><blockquote type="cite"><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a><br></blockquote><blockquote type="cite"><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">gmx-developers mailing list<br></blockquote><blockquote type="cite"><a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br></blockquote><blockquote type="cite"><a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br></blockquote><blockquote type="cite">Please don't post (un)subscribe requests to the list. Use the<br></blockquote><blockquote type="cite">www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-----------------------------------------------<br></blockquote><blockquote type="cite">Erik Marklund, PhD<br></blockquote><blockquote type="cite">Dept. of Cell and Molecular Biology, Uppsala University.<br></blockquote><blockquote type="cite">Husargatan 3, Box 596, 75124 Uppsala, Sweden<br></blockquote><blockquote type="cite">phone: +46 18 471 6688 fax: +46 18 511 755<br></blockquote><blockquote type="cite"><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a><br></blockquote><blockquote type="cite"><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">gmx-developers mailing list<br></blockquote><blockquote type="cite"><a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br></blockquote><blockquote type="cite"><a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br></blockquote><blockquote type="cite">Please don't post (un)subscribe requests to the list. Use the<br></blockquote><blockquote type="cite">www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-----------------------------------------------<br></blockquote><blockquote type="cite">Erik Marklund, PhD<br></blockquote><blockquote type="cite">Dept. of Cell and Molecular Biology, Uppsala University.<br></blockquote><blockquote type="cite">Husargatan 3, Box 596, 75124 Uppsala, Sweden<br></blockquote><blockquote type="cite">phone: +46 18 471 6688 fax: +46 18 511 755<br></blockquote><blockquote type="cite"><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a><br></blockquote><blockquote type="cite"><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">gmx-developers mailing list<br></blockquote><blockquote type="cite"><a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br></blockquote><blockquote type="cite"><a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br></blockquote><blockquote type="cite">Please don't post (un)subscribe requests to the list. Use the<br></blockquote><blockquote type="cite">www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-----------------------------------------------<br></blockquote><blockquote type="cite">Erik Marklund, PhD<br></blockquote><blockquote type="cite">Dept. of Cell and Molecular Biology, Uppsala University.<br></blockquote><blockquote type="cite">Husargatan 3, Box 596, 75124 Uppsala, Sweden<br></blockquote><blockquote type="cite">phone: +46 18 471 6688 fax: +46 18 511 755<br></blockquote><blockquote type="cite"><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a><br></blockquote><blockquote type="cite"><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">gmx-developers mailing list<br></blockquote><blockquote type="cite"><a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br></blockquote><blockquote type="cite"><a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br></blockquote><blockquote type="cite">Please don't post (un)subscribe requests to the list. Use the<br></blockquote><blockquote type="cite">www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-----------------------------------------------<br></blockquote><blockquote type="cite">Erik Marklund, PhD<br></blockquote><blockquote type="cite">Dept. of Cell and Molecular Biology, Uppsala University.<br></blockquote><blockquote type="cite">Husargatan 3, Box 596, 75124 Uppsala, Sweden<br></blockquote><blockquote type="cite">phone: +46 18 471 6688 fax: +46 18 511 755<br></blockquote><blockquote type="cite"><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a><br></blockquote><blockquote type="cite"><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">gmx-developers mailing list<br></blockquote><blockquote type="cite"><a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br></blockquote><blockquote type="cite"><a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br></blockquote><blockquote type="cite">Please don't post (un)subscribe requests to the list. Use the<br></blockquote><blockquote type="cite">www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br></blockquote><br><br><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br><br>post-doctoral researcher<br>Molecular Dynamics Group<br>* Groningen Institute for Biomolecular Research and Biotechnology<br>* Zernike Institute for Advanced Materials<br>University of Groningen<br>The Netherlands<br>--<br>gmx-developers mailing list<br><a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>http://lists.gromacs.org/mailman/listinfo/gmx-developers<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to gmx-developers-request@gromacs.org.<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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 href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></div></span></div></span></span>
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