# [gmx-developers] Re: Force calculation

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 18 20:31:30 CEST 2006

```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                                     |
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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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