[gmx-users] Centering the membrane for gmx h2order

Mark Abraham mark.j.abraham at gmail.com
Mon Apr 2 17:45:16 CEST 2018


The trjconv tool has many options if you want to center on things before
you try your analysis. But consider carefully what you actually want to
compute as the "center of mass" of the membrane, and what that means as
lipids diffuse laterally over time.


On Sun, Apr 1, 2018, 23:12 Searle Duay <searle.duay at uconn.edu> wrote:

> Hi gmx users,
> I'm using gmx h2order for my lipid bilayer in water because I want to get
> the average cosθ of water molecules from the center of my bilayer. However,
> the membrane moves along the z-axis throughout the simulation, so I don't
> think that I am getting the correct results. Is there a way that I can
> center the bilayer similar to gmx density?
> Thank you!
> --
> Searle Aichelle S. Duay
> Ph.D. Student
> Chemistry Department, University of Connecticut
> searle.duay at uconn.edu
> --
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