[gmx-users] Re:Re: Recentering box after simulation of self-assembly of a bilayer (Justin A. Lemkul)

[maria goranovic]

Thank you Justin. The following option worked for me:

 -center -boxcenter zero -pbc mol

with the centering done around the lipid.

Sincerly

-Maria

Message: 3
> Date: Thu, 07 May 2009 07:41:50 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Recentering box after simulation of
>        self-assembly   of a    bilayer
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A02C8FE.4050109 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> maria goranovic wrote:
> > Please help !
> >
> > I ran a simulation of self-assembly of a DPPC lipid bilayer. At the end
> > of the simulation, I have a bilayer, but it is not at the center of the
> > box. Instead, it has two leaflets on each edge of the box separated by
> > water, with the bilayer normal along the x-axis. How can I realign this
> > trajectory, so that I can get the bilayer at the center of the box? It
> > will also be nice to be able to align the membrane with the z-axis as is
> > the norm. I have trialled and errored with many combinations of trjconv,
> > but none seems to work
> >
>
> Using trjconv -center should work.  If it doesn't, you'll have to provide
> the
> command lines that you have tried to get more useful advice.  Alignment
> with the
> z-axis may be tricky.  You could, in theory, dump out all the frames from
> the
> trajectory (or at least a subset) as .pdb/.gro files, use editconf to
> rotate all
> of them, then use trjconv to convert them to .trr/.xtc frames and
> concatenate
> with trjcat.  This procedure could easily be scripted for convenience.
>
> -Justin
>
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
> >
> >
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
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