# [gmx-developers] Re: Force calculation

Chenyue Xing cxing at ucdavis.edu
Wed Oct 18 21:11:32 CEST 2006

```>From Anton's advices, huge force comes from a small z (with relatively large
x and y), but real r is larger than z which should give a normal force. (If
I don't understand wrong, those particles are exposed to unreasonable close
interactions)

If z < cutoff but r2 > cutoff, it's not in the neighborlist (a)
If z > cutoff, it's anyway not in the neighborlist (b)
only real r2<cutoff will appear in neighborlist. (c)

Currently, only type (c) is in the neighborlist. Some border case of type
(a) (relatively large x,y enter the neighborlist) seems to cause problems.
So might be a good trial to eliminate those?

On 10/18/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Chenyue Xing wrote:
> > Yeah. I printed r^2 out as well as all Zs. r^2 is really calculated
> > based on Z.
>
> i am talking about the real r2, for those particles not in the
> neighborlist. you have to modify neigborsearching as well.
>
>
> > 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
> > <mailto: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>
> >      > <mailto:feenstra at few.vu.nl <mailto:feenstra at few.vu.nl>>> wrote:
> >      >
> >      >     Chenyue Xing wrote:
> >      >     [...]
> >      >      > Thank you for your discussion and I hope I can provide
> >      >     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> <mailto:Feenstra at few.vu.nl
> >     <mailto:Feenstra at few.vu.nl>> -
> >      >     www.few.vu.nl/~feenstra/ <http://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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> >      >
> >
> ------------------------------------------------------------------------
> >      >
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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
> >     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
> >     <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
> >
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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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