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" <jalem...@vt.edu> > Subject: Re: [gmx-users] Recentering box after simulation of > self-assembly of a bilayer > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4a02c8fe.4050...@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 > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > ======================================== > > 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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