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. <br><br>if i try pbc nojump, the lipids drift far away from the box in the xy plane<br>
<br><div class="gmail_quote">On Fri, Jul 3, 2009 at 12:00 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Today's Topics:<br>
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1. Re: how to center a MARTINI trajectory so that the lipid<br>
bilayer remains at the center of the box (XAvier Periole)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 3 Jul 2009 11:43:55 +0200<br>
From: XAvier Periole <<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>><br>
Subject: Re: [gmx-users] how to center a MARTINI trajectory so that<br>
the lipid bilayer remains at the center of the box<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:EEA7DAA1-6584-4AF0-8321-3FEA30A413F4@rug.nl">EEA7DAA1-6584-4AF0-8321-3FEA30A413F4@rug.nl</a>><br>
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<br>
What is the problem exactly? The two layers separate over the pbc?<br>
did you try a -pbc nojump prior the centering?<br>
<br>
On Jul 3, 2009, at 11:37 AM, maria goranovic wrote:<br>
<br>
> Dear All,<br>
><br>
> This has been discussed before for individual frames. But I am<br>
> having a problem in trying to center a trajectory so that the<br>
> bilayer remains at the center of the box. I have tried several<br>
> combinations, but none of the them work. In each case, the centering<br>
> and/or the fitting is done on the lipid bilayer itself.<br>
><br>
> trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br>
> center -boxcenter zero -pbc mol<br>
><br>
> this one works for one particular .gro file, but not for the whole<br>
> trajectory. I tried all of the following, but none of them work.<br>
> What is the solution ?<br>
><br>
><br>
> trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br>
> center -boxcenter zero<br>
> trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc<br>
> mol -boxcenter zero<br>
> trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc<br>
> mol -center<br>
> trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br>
> pbc mol -fit trans<br>
> trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br>
> pbc mol -fit trans -center<br>
> trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -<br>
> pbc mol -fit trans -center -boxcenter zero<br>
> trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit<br>
> trans<br>
> trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit<br>
> progressive<br>
><br>
> --<br>
> Maria G.<br>
> Technical University of Denmark<br>
> Copenhagen<br>
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End of gmx-users Digest, Vol 63, Issue 11<br>
*****************************************<br>
</blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br>