[gmx-developers] external potential ?

[Pim Schravendijk]

> If it is that simple you might want to implement it in the update code:
>
> if (x[i][ZZ] > L) {
>   x[i][ZZ] = 2*L-x[i][ZZ];
>   v[i][ZZ] *= -1;
> }
> and similar for zero.

Hmm, this would however create a fully-elastic wall if I see it correctly,
which is not really what I had in mind. I preferrably want to exclude the
energies between atoms and their minimum image neighbours* at the other
side of z=0,L out of my energy calculation, or at least out of the force
calculation. Just not putting them in the neigbour list during the 
neighbour search would seem the most elegant solution to this imho.

Then, an external potential should represent a hard wall, with a potential
going to infinity as x[i][ZZ] reaches z=0 or L. But how to do that we 
already resolved in the previous mails.

Greetings, Pim

*) forgot that word in my previous explanation, sorry for the possible 
confusion

--
Pim Schravendijk - PhD Student
Max Planck Institute for Polymer Research
http://www.mpip-mainz.mpg.de/~schraven/