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

[Merril Mathew]

Thanks Catarina.

On 16 Mar 2017 10:53 a.m., "Catarina A. Carvalheda dos Santos" <
c.a.c.dossantos at dundee.ac.uk> wrote:

> 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
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