Hello,
I'm using the MC optimizer to optimize protein complexes represented by
spheres. My script loops through various sets of restraints (either
distance or MS-connectivity) and generates an ensemble of structures for
each restraint set. My problem is that the speed of the optimizer changes
drastically each time over the loop, and there is no correlation between
the complexity of the restraint set and the speed of the optimizer. The
speed usually varies between 10 and 30 models per second, but will
sometimes slow to 1 model/10minutes forces me to terminate the script.
I always initialize each optmization cycle with new random coordinates, so
I know I'm not simply getting stuck in a local minima, and I know the
restraint sets themselves are all fine since I could loop over the same
restraint set many times and the speed would change unpredictably. I've
also tried setting up a completely new model instance for each restraint
set, which doesn't solve the problem either.
for restraint set:
for oc in range(self.optimization_cycles):
for particle in self.system.ds: ## RANDOMIZE COORDINATES
init_coors = IMP.algebra.get_random_vector_in(self.system.bb
)
particle.set_coordinates(init_coors)
T = self.initial_temperature
for mc in range(self.mc_cool_cycles): ## DO THE ANNEALING MC
T = 0.99*T
self.optimizer.set_kt(T)
self.optimizer.optimize(self.mc_cool_steps)
Any input is greatly appreciated.
Joe
--
Joseph D. Eschweiler
Ph.D. Candidate | Ruotolo Group
Department of Chemistry
University of Michigan
