Hello Xavier, and sorry to bump in. I am also having that same issue just as Maria described - could you please explain in a bit more details why does that happen?
I mean, why does the membrane move along z-axis, and how to solve/avoid it? Thanks a lot, -Shay _____ From: [email protected] [mailto:[email protected]] On Behalf Of XAvier Periole Sent: Friday, July 03, 2009 12:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Re: how to center a MARTINI trajectory so that thelipid bilayer remains at the center of the box (XAvier Periole) This sounds pretty bad! You have a drift of your all system apparently ... Did you not remove the COM of your system? For membranes it is often recommended to remove the water and the lipid bilayer separately. The might drift one from the other. On Jul 3, 2009, at 12:19 PM, maria goranovic wrote: 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
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