[gmx-users] Lipid head movement normal to monolayer.

[Catarina A. Carvalheda dos Santos]

Hey,

I'm not sure about lipid headgroups "emersing" "into water". Maybe
calculate the average and individual positions of the P and/or N atoms in
the z axis for each frame. It's normal that there are some fluctuations
though.

Anyways, if you want to compare the movement of each lipid molecule in
relation to the initial configuration I guess you can use g_rms (and use
the initial conformation as reference).

Hope this helps.

Regards,

On 15 March 2017 at 21:28, Merril Mathew <mmathe01 at mail.bbk.ac.uk> wrote:

> Dear all,
>
> I want to calculate how much my lipid heads emerse into water in a
> monolayer after simulation. I want to compare the movement of the lipids
> from the intial conformation to the final conformation. Is there a way to
> calculate such movement using GROMACS?
>
> Merril.
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-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK