<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear Gormacs User,<br><br>I have now created a new tpr in which the protein is centered.<br>trjconv -f promd.xtc -s tprdodecasolv.tpr -center -boxcenter tric -pbc mol -ur compact -o center.xtc<br>trjconv -s tprdodecasolv.tpr -fit rot+trans -f center.xtc -o fit.xtc<br><br>I see the dimer getting split in some of the frames of fit.xtc.?<br><br>>> 2. The box seems to shift from one corner to the center. Especially for the<br>>> duration 8-12 ns (my restart run)<br><br>>What do you mean with this?<br><br>I actually see my dodeca box jumping from one end of the viewer to another ( in VMD as well as in ngmx)<br><br>thanks for your attention and reply.<br><br>regards<br>nahren<br><br><br>--- On <b>Wed, 4/22/09, Tsjerk Wassenaar <i><tsjerkw@gmail.com></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left:
5px; padding-left: 5px;"><br>From: Tsjerk Wassenaar <tsjerkw@gmail.com><br>Subject: Re: [gmx-users] -center -fit dodecahedron : dimer<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Wednesday, April 22, 2009, 2:50 PM<br><br><div class="plainMail">Hi Nahren,<br><br>> trjconv -f promd.trr -s proem.tpr -pbc nojump -o nojump.xtc<br>> trjconv -f nojump.xtc -s proem.tpr -pbc mol -ur compact -center -boxcenter tric -o center.xtc<br>> trjconv -f center.xtc -s proem.tpr -fit rot+trans -o fit.xtc<br><br>> 1. The above procedures does not center the molecule in the box.<br><br>You first center and then do a fit. The fitted trajectory will only be<br>centered if the reference (proem.tpr) is (and then you can skip the<br>second step anyway).<br><br>> 2. The box seems to shift from one corner to the center. Especially for the<br>> duration 8-12 ns (my restart run)<br><br>What do you mean with
this?<br><br>Cheers,<br><br>Tsjerk<br><br><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8<br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931<br>F: +31-30-2537623<br>_______________________________________________<br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org"
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