[gmx-users] query regarding self-assembly process

Mark Abraham mark.abraham at anu.edu.au
Sat Jun 16 06:52:57 CEST 2007

> 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


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