[gmx-developers] Re: Force calculation

[Chenyue Xing]

Hi David,

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.
> ________________________________________________________________________
> 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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