On Mar 30, 2008, at 8:40 PM, Daniel Russel wrote: >> philosophically, i agree with with daniel that the name 'Harmonic' >> requires a spring constant. >> to make everybody happy, i would propose a new name for functions >> that call the harmonic functions, but have spatial parameters as an >> input. for example LogGauss, LogUpperDistanceGauss or whatever you >> agree with. >> is anybody be willing to contribute something like that to the >> kernel (i am an official application guy, so the kernel is 'tabu' >> for me)? i think the current workaround, i.e. introducing scaling >> parameters through the back-door, is a bit unsatisfactory and will >> confuse most users. > I agree that adding a new set of scoring functions in the most > satisfactory response. There is still the question of whether we > should use straight standard deviation (so the energy is simply > delta^2/ (2*sigma^2)) or have scaling factors as in the old harmonic. agreed. strictly speaking, the scaling is only relevant if one uses MD for optimization. probably, it is most convenient to include the scaling for most users. but both is fine with me, as long as it is documented. other opinions?
f