Attached is a patch which corrects the math in DistanceRestraint. Currently if the interparticle distance is zero (or very near zero) DistanceRestraint pretends that the particles are randomly placed in near proximity, so that a random distance and derivatives are returned. This is because the derivatives of the distance at zero are undefined (the math is 0/0).

IMHO, this behavior is flawed, because the score of a given state should always be the same - and the scoring function should be deterministic. Any necessary randomization of the system should be introduced by perturbing the system state before an optimization, not by having the scoring function return random values. (The current behavior also makes it impossible to introduce a distance restraint with zero mean, to force two particles to be colocated.)

This patch returns a zero derivative for zero distance, which is at least consistent with every molecular mechanics package I've seen.

Ben