[gmx-users] Center on bilayer

Gmx QA gmxquestions at gmail.com
Wed Nov 16 20:12:08 CET 2016

I realize this has been discussed at length before, but I can't for the
life of me get it to work.

I have a system where I want to assemble a bilayer from randomly placed
lipids (using charmm36 that is not the main point).

After about 50 ns I have what seems to be two (rough) leaflets being
formed, but of course one leaflet sits at the "top" of the box and the
other at the bottom, with water in between.

I want a trajectory with the bilayer in the center.

Reading some of the previous suggestions has led me to understand that
simply using -center on the entire POPC group will not work, since they in
fact already have their geometrical center in the box.

I then did try and select a single atom from of the tails in an arbitrary
lipid (the C18-atom) and use that as a centering group, but that does not
work either (in the sense that the two leaflets are still separated by a
chunk of water).

Is there any other way of accomplishing this, such as e.g. shifting the
center of the box or so?


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