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<p class=MsoNormal dir=LTR><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>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? <o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>I mean, why does the membrane move along z-axis, and how to
solve/avoid it?<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>Thanks a lot,<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>-Shay<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
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<p class=MsoNormal dir=LTR><b><font size=2 face=Tahoma><span style='font-size:
10.0pt;font-family:Tahoma;font-weight:bold'>From:</span></font></b><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <b><span style='font-weight:bold'>On
Behalf Of </span></b>XAvier Periole<br>
<b><span style='font-weight:bold'>Sent:</span></b> Friday, July 03, 2009 12:27
PM<br>
<b><span style='font-weight:bold'>To:</span></b> <st1:PersonName w:st="on">Discussion
list for GROMACS users</st1:PersonName><br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [gmx-users] Re: how
to center a MARTINI trajectory so that thelipid bilayer remains at the center
of the box (XAvier Periole)</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
</div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>This sounds pretty bad! You have a drift of your all
system apparently ... <o:p></o:p></span></font></p>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Did you not remove the COM of your system? <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>For membranes it is often recommended to remove the
water and the <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>lipid bilayer separately. The might drift one from the
other.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<div>
<div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>On Jul 3, 2009, at 12:19 PM, maria goranovic wrote:<o:p></o:p></span></font></p>
</div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'><br>
<br>
<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>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<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>On Fri, Jul 3, 2009 at 12:00 PM, <<a
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>
wrote:<o:p></o:p></span></font></p>
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Today's Topics:<br>
<br>
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: <st1:PersonName w:st="on">Discussion list for GROMACS users</st1:PersonName>
<<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>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes<br>
<br>
<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>
> <st1:PlaceName w:st="on">Technical</st1:PlaceName> <st1:PlaceType w:st="on">University</st1:PlaceType>
of <st1:country-region w:st="on"><st1:place w:st="on">Denmark</st1:place></st1:country-region><br>
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Maria G.<br>
<st1:PlaceName w:st="on">Technical</st1:PlaceName> <st1:PlaceType w:st="on">University</st1:PlaceType>
of <st1:country-region w:st="on"><st1:place w:st="on">Denmark</st1:place></st1:country-region><br>
<st1:City w:st="on"><st1:place w:st="on">Copenhagen</st1:place></st1:City><br>
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