<br>
Dear Anna,<br>
<br>
The option you want for trjconv is -pbc nojump<br>
This will remove jumps over the periodic boundaries. Alternatively you
can fit to a reference group, to keep the protein in a fixed position /
orientation (-fit rot+trans). Please also check the help of trjconv
(trjconv -h).<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 1/4/06, <b class="gmail_sendername"><a href="mailto:herbst@fhi-berlin.mpg.de">herbst@fhi-berlin.mpg.de</a></b> <<a href="mailto:herbst@fhi-berlin.mpg.de">herbst@fhi-berlin.mpg.de
</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">trjconv does not know this option<br><br>> use trjconv -center tric -f
in.xtc -o out.xtc<br>><br>> Yang Ye<br>> Nanyang Technolgoical University, Singapore<br>><br>> ----- Original Message ----<br>> From: Florian Haberl <<a href="mailto:Florian.Haberl@chemie.uni-erlangen.de">
Florian.Haberl@chemie.uni-erlangen.de</a>><br>> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Sent: Wednesday, January 04, 2006 7:16:40 PM<br>
> Subject: Re: [gmx-users] center of mass motion<br>><br>> hi<br>><br>> On Wednesday 04 January 2006 11:22, <a href="mailto:herbst@fhi-berlin.mpg.de">herbst@fhi-berlin.mpg.de</a> wrote:<br>>> Hi all,<br>
>><br>>> my protein is jumping out of the box during the simulation. I tried to<br>>> center it in the box using trjconv -pbc inbox -center, but when I look<br>>> at<br>>> the new trajectory, it is still leaving the box and I can't watch it.
<br>>> Am I doing something wrong ?<br>> Take a reference strucuture which is inside the box, normally the<br>> minimized em<br>> or pr file. ( trjconv -s file. ...)<br>><br>><br>>> And how can I constrain the center of mass motion in the simulation ?
<br>><br>><br>><br>>><br>>> Thanks,<br>>> Anna<br>>> _______________________________________________<br>>> gmx-users mailing list<br>>> <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
</a><br>>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>>> Please don't post (un)subscribe requests to the list. Use the<br>>> www interface or send it to
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>><br>> Greetings,<br>><br>> Florian<br>><br>> --<br>> -------------------------------------------------------------------------------
<br>> Florian Haberl<br>> Computer-Chemie-Centrum<br>> Universitaet Erlangen/ Nuernberg<br>> Naegelsbachstr 25<br>> D-91052 Erlangen<br>> Mailto: florian.haberl AT <a href="http://chemie.uni-erlangen.de">
chemie.uni-erlangen.de</a><br>> -------------------------------------------------------------------------------<br>> _______________________________________________<br>> gmx-users mailing list<br>> <a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>><br>><br>><br>> _______________________________________________<br>> gmx-users mailing list
<br>> <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please don't post (un)subscribe requests to the list. Use the
<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>><br><br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>