[gmx-developers] Re: Force calculation
David van der Spoel
spoel at xray.bmc.uu.se
Wed Oct 18 20:44:13 CEST 2006
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.
please reread carefully Antons comments.
> 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
> more info
> > 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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> --
> 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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