[gmx-users] simulations using structureless surface-2

Mark Abraham mark.abraham at anu.edu.au
Fri Jul 27 01:56:17 CEST 2007

> Dear gmx users,
> my apologies for the previous post. I will try to rephrase my problem.
> Is it possible to introduce a plane in a particular direction, for example
> in z direction, where molecules interact with it only based on the
> perpendicular distance between the molecules and the plane?

Yes, this is possible to do, but it is not implemented. Possibly something
in the distance restraints section may do what you want. See the manual.

> Is it also possible to specify the user defined potential for interaction
> between the plane and molecules?

Possible, but not implemented.

> The idea is to simulate a surface, for example a graphite surface, but
> rather than using a detailed atomistic model for it, I would like to
> represent it by using a plane with some interaction potentials.

If you're not dealing with only a handful of species interacting with such
a surface, you might want to write such code yourself. Otherwise, you'll
need to get your hands very dirty with GROMACS.


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