<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>16 apr 2012 kl. 12.09 skrev Berk Hess:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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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></div></blockquote><div><br></div><div>Yes it does. I tried to find this issue, but failed. What is its id?</div><div><br></div><div>Best,</div><div><br></div><div>Erik</div><br><blockquote type="cite"><div bgcolor="#FFFFFF" text="#000000">
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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>
<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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<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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