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
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