<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>This sounds pretty bad! You have a drift of your all system apparently ... <div>Did you not remove the COM of your system? </div><div>For membranes it is often recommended to remove the water and the </div><div>lipid bilayer separately. The might drift one from the other.</div><div><br><div><div><div>On Jul 3, 2009, at 12:19 PM, maria goranovic wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Well the bilayer drifts down in the z-direction, and eventually the leaflets almost separate, with each leaflet being on opposite ends of the box. <br><br>if i try pbc nojump, the lipids drift far away from the box in the xy plane<br> <br><div class="gmail_quote">On Fri, Jul 3, 2009 at 12:00 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> Send gmx-users mailing list submissions to<br> <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> <br> To subscribe or unsubscribe via the World Wide Web, visit<br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> or, via email, send a message with subject or body 'help' to<br> <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br> <br> You can reach the person managing the list at<br> <a href="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</a><br> <br> When replying, please edit your Subject line so it is more specific<br> than "Re: Contents of gmx-users digest..."<br> <br> <br> Today's Topics:<br> <br> 1. Re: how to center a MARTINI trajectory so that the lipid<br> bilayer remains at the center of the box (XAvier Periole)<br> <br> <br> ----------------------------------------------------------------------<br> <br> Message: 1<br> Date: Fri, 3 Jul 2009 11:43:55 +0200<br> From: XAvier Periole <<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>><br> Subject: Re: [gmx-users] how to center a MARTINI trajectory so that<br> the lipid bilayer remains at the center of the box<br> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br> Message-ID: <<a href="mailto:EEA7DAA1-6584-4AF0-8321-3FEA30A413F4@rug.nl">EEA7DAA1-6584-4AF0-8321-3FEA30A413F4@rug.nl</a>><br> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes<br> <br> <br> What is the problem exactly? The two layers separate over the pbc?<br> did you try a -pbc nojump prior the centering?<br> <br> On Jul 3, 2009, at 11:37 AM, maria goranovic wrote:<br> <br> > Dear All,<br> ><br> > This has been discussed before for individual frames. But I am<br> > having a problem in trying to center a trajectory so that the<br> > bilayer remains at the center of the box. I have tried several<br> > combinations, but none of the them work. In each case, the centering<br> > and/or the fitting is done on the lipid bilayer itself.<br> ><br> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br> > center -boxcenter zero -pbc mol<br> ><br> > this one works for one particular .gro file, but not for the whole<br> > trajectory. I tried all of the following, but none of them work.<br> > What is the solution ?<br> ><br> ><br> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br> > center -boxcenter zero<br> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc<br> > mol -boxcenter zero<br> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc<br> > mol -center<br> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br> > pbc mol -fit trans<br> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br> > pbc mol -fit trans -center<br> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br> > pbc mol -fit trans -center -boxcenter zero<br> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit<br> > trans<br> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit<br> > progressive<br> ><br> > --<br> > Maria G.<br> > Technical University of Denmark<br> > Copenhagen<br> > _______________________________________________<br> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> > <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.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<br> > posting!<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> > Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br> <br> <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://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.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> <br> End of gmx-users Digest, Vol 63, Issue 11<br> *****************************************<br> </blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br> _______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php</blockquote></div><br></div></div></body></html>