[gmx-users] query regarding self-assembly process

[Mark Abraham]

> Dear gromacs users,
>      I am trying simulate self-assembly of protein on
> gold surface. To get an idea, I was looking for
> various literatures which this kind of self-assembly.
> Many of them reports that they used periodic boundary
> condition in X and Y diection(gold-surface is in one
> extreme of z direction) and then used a repulsive(
> reflecting) wall opposite to the gold surface.
>  But, I was wondering if some one can explain  the
> algorithm for  how to create wall which will be
> repulsive as well as reflective.

Seems to me that a repulsive wall just about *is* a reflective wall, so a
1/r function or similar would work. The trick is what happens when a
particle has enough velocity to pass the wall, if ever... now you need to
do a clipping test and handle the reflection. If you had a large enough
potential ramp up to the wall, then this would be a non-problem in
practice.

Mark