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

[Neha Shafique]

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!

Best,
Neha