[gmx-developers] Re: Force calculation

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 17 09:52:49 CEST 2006

Chenyue Xing wrote:
> Plus, with the first case r=z running EM (steep)
> the result gives potential energy reaches xxx (a reasonable number) and 
> max force = inf on atom xxxx, norm of force = xxx ( a huge number).
> while with force in z component only (set fx, fy to 0, actually) running 
> EM (steep)
> potential energy, max force and norm of force are all reasonable.

The two things you compare are not identical. You can have z = 0, but 
that does not mean that r = 0. Since in general the forces are computed 
as 1/r^n having z very small will lead to singularities. So please 
specify what kind of potential you want to use that is Z dependent only.

David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se

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