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

[Shay Amram]

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: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
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, <gmx-users-request at gromacs.org> wrote:

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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
> _______________________________________________
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-- 
Maria G.
Technical University of Denmark
Copenhagen
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