Thank you Justin. The following option worked for me:<br><br> -center -boxcenter zero -pbc mol<br><br>with the centering done around the lipid.<br><br>Sincerly<br><br>-Maria<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Message: 3<br>
Date: Thu, 07 May 2009 07:41:50 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Recentering box after simulation of<br>
self-assembly of a bilayer<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:4A02C8FE.4050109@vt.edu">4A02C8FE.4050109@vt.edu</a>><br>
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<br>
maria goranovic wrote:<br>
> Please help !<br>
><br>
> I ran a simulation of self-assembly of a DPPC lipid bilayer. At the end<br>
> of the simulation, I have a bilayer, but it is not at the center of the<br>
> box. Instead, it has two leaflets on each edge of the box separated by<br>
> water, with the bilayer normal along the x-axis. How can I realign this<br>
> trajectory, so that I can get the bilayer at the center of the box? It<br>
> will also be nice to be able to align the membrane with the z-axis as is<br>
> the norm. I have trialled and errored with many combinations of trjconv,<br>
> but none seems to work<br>
><br>
<br>
Using trjconv -center should work. If it doesn't, you'll have to provide the<br>
command lines that you have tried to get more useful advice. Alignment with the<br>
z-axis may be tricky. You could, in theory, dump out all the frames from the<br>
trajectory (or at least a subset) as .pdb/.gro files, use editconf to rotate all<br>
of them, then use trjconv to convert them to .trr/.xtc frames and concatenate<br>
with trjcat. This procedure could easily be scripted for convenience.<br>
<br>
-Justin<br>
<br>
> --<br>
> Maria G.<br>
> Technical University of Denmark<br>
> Copenhagen<br>
><br>
><br>
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<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
</blockquote></div><br>