[gmx-users] Coordinate File and Origin in Gromacs // Separating Bilayer Leaflets

Neha Shafique nshafique at wesleyan.edu
Thu Sep 25 18:38:59 CEST 2014

Hi everybody,

I am running Gromacs 4.6, and simulating a Martini bilayer. For some of the
analysis, I want to separate the bilayer into leaflets and analyze their
data individually. I was wondering if Gromacs had a script or tool that
would allow me to do that.

If there is no pre-existing tool, I would need to write a script myself.
However, I realized that I don't know how Gromacs prints out coordinates in
the trajectory. I read the .trr files, and it didn't really say very much.
Is the origin in the 'middle' of the box, is it in a corner? Can I change
the convention? Please let me know if you have any suggestions!


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