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

machuque machuque at itqb.unl.pt
Thu May 7 15:30:35 CEST 2009

At 12:35 PM 5/7/2009, you 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

Hi Maria,

One simple trick can be the use of only 1 atom as a reference for 
"trjconv -center".

You can make a small index.ndx (even by hand) with only 1 atom 
number. Choose for instance the last atom (which should be closer to 
the center of the membrane) of the first lipid in your system.

When running "trjconv -center" choose this atom to center. The system 
will not be perfectly centered to the z-axis (you can try afterwards 
a -center command of the whole bilayer), but it will be just fine for 

This way, you will solve many problems that won't be solved by giving 
the whole bilayer.



Miguel Machuqueiro
ITQB-Instituto de Tecnologia Química e Biológica
Universidade Nova de Lisboa - 6º Floor (Room 601)
Av. da República, EAN, 2780-157 Oeiras, Portugal
Tel. : +351 214469618 /Mobile: +351 96 7562285
E-mail: machuque at itqb.unl.pt
www1: http://www.itqb.unl.pt/simulation
www2: http://www.itqb.unl.pt/~machuque
www3: http://www.linkedin.com/in/miguelmachuqueiro

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