[gmx-developers] Re: Force calculation
cxing at ucdavis.edu
Tue Oct 17 10:35:32 CEST 2006
I want to use just a LJ potential for a z-dependent only interaction. I
noticed that 1/r^n and 1/r^(n+1) are used for energy and force calculation
so I tried to set r = z only.
Hope you can give me more advices.
Thank you very much!
On 10/17/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 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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