[gmx-users] Smooth surface

[Tsjerk Wassenaar]

Hi Alex,

I think you're best off describing the wall with particles. You can
freeze them to a specific position (make it a freeze-group) and set
all interactions between them to zero. You can tune your particles to
be hydrophilic or hydrophobic.

Hope it helps,

Tsjerk

On 11/7/06, Alexei Krukau <alex at heineken.chemie.uni-dortmund.de> wrote:
> On Tuesday 07 November 2006 01:41, Mark Abraham wrote:
> > Alexei Krukau wrote:
> > > Dear Gromacs users,
> > > I would like to ask, if there is a possibility to create a smooth
> > > (unstructured) hydrophobic or hydrophilic wall in Gromacs?
> >
> > I think not, but it is hard for me to guess what you are trying to do.
> > If you explain more clearly, other people may be better able to help you.
> >
> > Mark
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> I would like to make a slit-like smooth pore, to calculate adsorption of some
> small peptides from liquid water on the pore walls. Hydrophilicity or
> hydrophobicity of the walls should be tunable.
> --
> Alex Krukau
> Physical Chemistry II a
> University of Dortmund
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-- 
Tsjerk A. Wassenaar, Ph.D.
post-doc
NMR, Utrecht University,
Padualaan 8,
3584 CH Utrecht, the Netherlands
P: +31-30-2539931
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