I remember having a similar issue a long time ago. If I remember correctly, the culprit was a bad parametrization of the Langevin piston. Maybe you should specified how the pressure is controlled, as well as how you managed the center of mass motions in you dynamics.
Nicolas > 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. > > if i try pbc nojump, the lipids drift far away from the box in the xy > plane > > On Fri, Jul 3, 2009 at 12:00 PM, <[email protected]> wrote: > >> Send gmx-users mailing list submissions to >> [email protected] >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> or, via email, send a message with subject or body 'help' to >> [email protected] >> >> You can reach the person managing the list at >> [email protected] >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of gmx-users digest..." >> >> >> Today's Topics: >> >> 1. Re: how to center a MARTINI trajectory so that the lipid >> bilayer remains at the center of the box (XAvier Periole) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 3 Jul 2009 11:43:55 +0200 >> From: XAvier Periole <[email protected]> >> Subject: Re: [gmx-users] how to center a MARTINI trajectory so that >> the lipid bilayer remains at the center of the box >> To: Discussion list for GROMACS users <[email protected]> >> Message-ID: <[email protected]> >> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes >> >> >> What is the problem exactly? The two layers separate over the pbc? >> did you try a -pbc nojump prior the centering? >> >> On Jul 3, 2009, at 11:37 AM, maria goranovic wrote: >> >> > Dear All, >> > >> > This has been discussed before for individual frames. But I am >> > having a problem in trying to center a trajectory so that the >> > bilayer remains at the center of the box. I have tried several >> > combinations, but none of the them work. In each case, the centering >> > and/or the fitting is done on the lipid bilayer itself. >> > >> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx - >> > center -boxcenter zero -pbc mol >> > >> > this one works for one particular .gro file, but not for the whole >> > trajectory. I tried all of the following, but none of them work. >> > What is the solution ? >> > >> > >> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx - >> > center -boxcenter zero >> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc >> > mol -boxcenter zero >> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc >> > mol -center >> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx - >> > pbc mol -fit trans >> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx - >> > pbc mol -fit trans -center >> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx - >> > pbc mol -fit trans -center -boxcenter zero >> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit >> > trans >> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit >> > progressive >> > >> > -- >> > Maria G. >> > Technical University of Denmark >> > Copenhagen >> > _______________________________________________ >> > gmx-users mailing list [email protected] >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at http://www.gromacs.org/search before >> > posting! >> > Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to [email protected]. >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> ------------------------------ >> >> _______________________________________________ >> gmx-users mailing list >> [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> >> End of gmx-users Digest, Vol 63, Issue 11 >> ***************************************** >> > > > > -- > Maria G. > Technical University of Denmark > Copenhagen > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- [ Nicolas Sapay - Post-Doctoral Fellow ] CERMAV - www.cermav.cnrs.fr BP53, 38041 Grenoble cedex 9, France Phone: +33 (0)4 76 03 76 44 _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
