Daniel Russel wrote: >> Most physics-based scores are interaction energies between pairs of >> particles. But not all of course, otherwise this would be a solved >> problem already. > Sure, but for what we do (namely, not gravitation), the number of pairs > scales linearly with the number of atoms rather than quadratically > (since we have terms with finite cutoffs and packing constraints).
That is not true for Modeller-style homology-derived restraints, as one example.
> Rescaling a physics forcefield is harmless if all you are interesting in > doing is preserving minima.
Of course, but rescaling different parts of the forcefield by different amounts (e.g. bond terms vs. torsions, since the latter act on twice as many atoms) will really break things, and that was what I read your proposal as.
> That said, looking like existing physics > force fields is a reasonable criteria. But that requires that the other > terms scale with the number of atoms too (since all of the force fields > have finite cutoffs).
Molecular mechanics people have worked with such nonbonded interactions in their forcefields for many years: the effects of such cutoffs on the energies and dynamics are well understood. I don't think the same could be said for a rescaled term. This is why I suggest rescaling terms such as EM and SAXS rather than sterics and nonbonds.
Ben