[gmx-developers] Re: Force calculation
feenstra at few.vu.nl
Wed Oct 18 09:44:55 CEST 2006
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 ;-)
| | |
| _ _ ___,| 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 - www.few.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" (RHCP) |
More information about the gromacs.org_gmx-developers