[gmx-users] rotate trajectory from self-assembly of lipid bilayer

maria goranovic mariagoranovic at gmail.com
Tue Mar 24 12:29:08 CET 2009

Dear Friends

I have run a simple self-assembly simulation of a lipid bilayer. When I look
at the trajectory, the bilayer normal is aligned along the y-axis, and the
bilayer is not centered to the middle of the box, but towards the edge of
the box. So, the bilayer is split into its periodic image. I was wondering
what would be a good way to center the bilayer in the middle, and perhaps
align it along the y-axis too? I know this can be done for a single .gro
file using editconf, but how does one to it for a trajectory. I have tried
various combinations of -center (zero, rect, tric) and -fit (trans,
rot+trans), but nothing seems to work perfectly. I am using 3.3.1

Thanking you


Maria G.
Technical University of Denmark
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