Daniel Russel wrote:
So lets look at evaluating an excluded volume potential for all nearby pairs.Maybe some pseudocode would elucidate this.
...OK, looks reasonable, but could you show it with derivatives as well? I want to see how you propose combining these.
If we decided we want to move to a realish Leonard Jones potential
The reason I chose a harmonic term for the example is because both the mean and the standard deviation would have to be tweaked, and I don't see how you propose to do that with your proposal. I don't doubt that you can write a 6-12 term, but you cheated and changed the example. ;) (And it's odd that you say LJ isn't a simple function of distance, because Modeller does have a 6-12 math form, so there's nothing to stop you restraining an angle with a 6-12 form if you were sufficiently inclined.)
Ben -- ben@salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle