[gmx-users] Smooth surface

[Alexei Krukau]

On Tuesday 07 November 2006 08:46, David van der Spoel wrote:
> Tsjerk Wassenaar wrote:
> > 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,
>
> If that really is not what you want, then please write down some
> equations how you would treat a hydrophilic wall. Just a Lennard Jones
> is not very complicated, and we have actually done something like that
> in the past (Wensink et al. Langmuir 16 (2000), p. 7392).
I need Lennard-Jones interactions in Z direction between walls and Oxygens of 
water molecules. And second, repulsion function (also in Z direction) between 
atoms of peptides and walls. I think that it is possible to introduce 
periodic boundary conditions only in x and y directions? 
-- 
Alex Krukau
Physical Chemistry II a
University Dortmund
tel: + 49 231 755 3938
fax: + 49 231 755 3937