[ODE] Remote forces using ODE optimization

[Sergey Kurdakov]

Hello Kevin,

just a thought...

I would suggest you to use octree.
there are implementations on the net - use google.

you may have a sort of  index for each Protein and when it moves to re assign to different octre cells.
then
you may even compute 'average mass' for distant cells.

and you will be computing force in a cell where  given protein is situated ( I would suggest to compute force from all proteins in
surrounding cells) the forces from outside this neigbourhood coud be either averaged or omited.

so basicaly - keep your approach

> So I programmed my own function wich takes every protein and calculate
> the forces with all the other proteins. (n*(n-1)/2 complexity)

just keep proteins in octree and 'cull' far proteins from computation accordingly

Sergey