[gmx-developers] Re: Force calculation

Chenyue Xing cxing at ucdavis.edu
Wed Oct 18 20:34:29 CEST 2006

```Yeah. I printed r^2 out as well as all Zs. r^2 is really calculated based on
Z.
So there's a r^2 calculation in neighborsearching too and it's somehow used
in table look-up?

On 10/18/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Chenyue Xing wrote:
> > Hi Anton,
> >
> > Thanks for the nice suggestions.
> > As for the first possibility, I've been investigating and printed out
> > all the zi, zj, but haven't got a clue yet.
> > As for the 2nd, the modified code still works in the same manner, that
> > rsq = z^2 and then take the sqrt, so a negative r should not be a
> problem.
> >
>
>
> have you checked r2 as well? I'm pretty sure it is the nieghboursearching.
>
> > If you have any other guess, please let me know. That will help a lot.
> >
> > Thank you !
> > Chenyue
> >
> >
> > On 10/18/06, *Anton Feenstra* <feenstra at few.vu.nl
> > <mailto:feenstra at few.vu.nl>> wrote:
> >
> >     Chenyue Xing wrote:
> >     [...]
> >     soon so
> >      > that you might be able to give me more advices.
> >
> >     There are two problems I can think of that may be bothering you.
> >     First is related to what David already mentioned: if you have an
> LJ-type
> >     interaction and your z becomes very small, the resulting force is
> HUGE.
> >     This can happen suddenly in your case when a particle enters the
> cutoff
> >     (as determined by the neighbourlist update), with relatively large x
> or
> >     y, but small z.
> >     Second is that r=z is not really equivalent to the 3D case, because
> >     your
> >     r can become negative (I haven't looked at the code, but I suspect
> >     something like z=zi-zj for particle i and j). In the 3D case, you
> have
> >     the squares and square-root. I can imagine that a negative r will
> not be
> >     present in the lookup table ;-)
> >
> >
> >     --
> >     Groetjes,
> >
> >     Anton
> >
> >     _____________
> _______________________________________________________
> >     |
> |                                                       |
> >     |  _   _  ___,| K. Anton
> Feenstra                                     |
> >     | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit
> Amsterdam   |
> >     |(   |   )| | | De Boelelaan 1083 - 1081A HV Amsterdam -
> Netherlands  |
> >     | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room
> P440 |
> >     |             | Feenstra at few.vu.nl <mailto:Feenstra at few.vu.nl> -
> >     www.few.vu.nl/~feenstra/ <http://www.few.vu.nl/~feenstra/>         |
> >     |             | "If You See Me Getting High, Knock Me Down"
> (RHCP)    |
> >
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>
> --
> 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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