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
> 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
> 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.
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle