Daniel Russel wrote: > Now that I actually tried to use it, I find the Harmonic class a bit > odd. For one thing the parameter is called "standard deviation" or > something, which doesn't mean anything for a harmonic.
Read the '93 Modeller paper, and perhaps also the appendices to the Modeller manual, and all will become clear.
> Secondly, once > you figure out what it is, it is multiplied by a many significant > figure constant before it is used (the documentation says this is for > modeller compatibility).
It has nothing to do with Modeller compatibility - that's sqrt(RT/2) where energy units are kcal/mol and T is 297.15K. If anything, that's a CHARMM/GROMOS compatibility thing. The documentation in the code is obviously nonsense, and my suspicion is that Bret "derived" this magic factor empirically, since it differs from the exact value.
> Do we really want this? In my mind the thing that makes the most sense > is to to have a the mean and the spring constant be the parameters and > to get rid of the odd multiplier.
The two are equivalent, of course. One is easier to use if you think in scoring-function space, and the other is easier to use if you think in coordinate space (e.g. harmonic restraint on a distance with a stdev of 0.1 will result in fluctuations of 0.1 at room temperature). I have no strong preference for either, since it is very very easy to interconvert them. Since we have a lot of code that relies on the existing behavior, we'll stick with it for now unless others would also prefer the kxx/2 form, in which case I'll update the code accordingly.
Ben