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

maria goranovic mariagoranovic at gmail.com
Thu May 7 13:35:15 CEST 2009

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

Maria G.
Technical University of Denmark
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