[gmx-users] Deuterium order parameter over area of membrane

Xavier Periole X.Periole at rug.nl
Mon Nov 10 09:48:46 CET 2008

On Mon, 10 Nov 2008 11:09:01 +0530
  "anirban polley" <polley.anirban at gmail.com> wrote:
> Hi,
>     I know that deuterium order parameter can be calculated by g_density
> but it calculate average deuterium order parameter of a type of lipid Vs.
> atom number of the tail of the lipid.
>     But I want to calculate deuterium order parameter fluctuation over the
> area. i.e., I want to know to calculate Scd per area of the membrane. Could
> you tell me how to do it.
You may want to generate an index that would give the lipids in the area
you are interested in. This would work for the thickness, the density and
S_CD. You'll need to make the index by a script of your own as make_ndx
does not select based on positions bu only on names etc. It is not difficult

> Thanks,
> Anirban
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XAvier Periole - PhD

- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands

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