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

[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
>
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>   1. Re: how to center a MARTINI trajectory so that the lipid
>      bilayer remains at the center of the box (XAvier Periole)
>
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> ----------------------------------------------------------------------
>
> 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
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> -- 
> Maria G.
> Technical University of Denmark
> Copenhagen
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