On 08/03/2009 02:49 PM, Daniel Russel wrote: > Who would find fast incremental evaluations useful? What are expected > scenarios? Import parts of the scenario are how many particles would > change each step and what sort of restraints would be used.
The classic use case is atomic-scale Monte Carlo - for example, in a protein containing N atoms, stereochemical restraints (e.g. bonds) and nonbonded restraints (e.g. electrostatics, van der Waals). With the simplest MC move set of "pick a single atom and displace it by a random amount" in order to get comparable sampling to M steps of dynamics you'd need M*N steps of MC. Obviously this is only computationally feasible if each score calculation for the MC simulation takes roughly 1/N times as long as the score for dynamics.
Ben