[gmx-users] Re: how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box (XAvier Periole)

[maria goranovic]

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, <gmx-users-request at gromacs.org> wrote:

> Send gmx-users mailing list submissions to
>        gmx-users at gromacs.org
>
> 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
>        gmx-users-request at gromacs.org
>
> You can reach the person managing the list at
>        gmx-users-owner at gromacs.org
>
> 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 <x.periole at rug.nl>
> 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 <gmx-users at gromacs.org>
> Message-ID: <EEA7DAA1-6584-4AF0-8321-3FEA30A413F4 at rug.nl>
> 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    gmx-users at gromacs.org
> > 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 gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090703/e16931da/attachment.html>