[gmx-developers] external potential ?

[David]

On Thu, 2004-02-12 at 20:27, Pim Schravendijk wrote:
> > 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.
> 
that you can do by adding a layer of vacuum beyond z=L which is larger
than the cut-off. 

my solution does represent an elastic wall. if you don't do that you
have to transfer energy between the wall and the particles...

> 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/
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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