[gmx-users] Recentering box after simulation of self-assembly of a bilayer

Justin A. Lemkul jalemkul at vt.edu
Thu May 7 13:41:50 CEST 2009

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.


> -- 
> 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


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