[gmx-developers] Re: Force calculation

[Anton Feenstra]

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   |
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