[gmx-users] Centering the membrane for gmx h2order

[Searle Duay]

Thank you very much for your help!

Searle

On Mon, Apr 2, 2018 at 11:45 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> 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.
>
> Mark
>
> 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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-- 
Searle Aichelle S. Duay
Ph.D. Student
Chemistry Department, University of Connecticut
searle.duay at uconn.edu