def benchmark(reference_system, positions, receptor_atoms, ligand_atoms, platform_name=None, annihilateElectrostatics=True, annihilateSterics=False, nsteps=500):
"""
Benchmark performance relative to unmodified system.
ARGUMENTS
reference_system (simtk.openmm.System) - the reference System object to compare with
positions - the positions to assess energetics for
receptor_atoms (list of int) - the list of receptor atoms
ligand_atoms (list of int) - the list of ligand atoms to alchemically modify
"""
# Create a factory to produce alchemical intermediates.
logger.info("Creating alchemical factory...")
initial_time = time.time()
factory = AbsoluteAlchemicalFactory(reference_system, ligand_atoms=ligand_atoms)
final_time = time.time()
elapsed_time = final_time - initial_time
logger.info("AbsoluteAlchemicalFactory initialization took %.3f s" % elapsed_time)
# Create an alchemically-perturbed state corresponding to nearly fully-interacting.
# NOTE: We use a lambda slightly smaller than 1.0 because the AlchemicalFactory does not use Custom*Force softcore versions if lambda = 1.0 identically.
lambda_value = 1.0 - 1.0e-6
alchemical_state = AlchemicalState(0.00, lambda_value, lambda_value, lambda_value)
alchemical_state.annihilateElectrostatics = annihilateElectrostatics
alchemical_state.annihilateSterics = annihilateSterics
platform = None
if platform_name:
platform = openmm.Platform.getPlatformByName(platform_name)
# Create the perturbed system.
logger.info("Creating alchemically-modified state...")
initial_time = time.time()
alchemical_system = factory.createPerturbedSystem(alchemical_state)
final_time = time.time()
elapsed_time = final_time - initial_time
# Compare energies.
timestep = 1.0 * units.femtosecond
logger.info("Computing reference energies...")
reference_integrator = openmm.VerletIntegrator(timestep)
if platform:
reference_context = openmm.Context(reference_system, reference_integrator, platform)
else:
reference_context = openmm.Context(reference_system, reference_integrator)
reference_context.setPositions(positions)
reference_state = reference_context.getState(getEnergy=True)
reference_potential = reference_state.getPotentialEnergy()
logger.info("Computing alchemical energies...")
alchemical_integrator = openmm.VerletIntegrator(timestep)
if platform:
alchemical_context = openmm.Context(alchemical_system, alchemical_integrator, platform)
else:
alchemical_context = openmm.Context(alchemical_system, alchemical_integrator)
alchemical_context.setPositions(positions)
alchemical_state = alchemical_context.getState(getEnergy=True)
alchemical_potential = alchemical_state.getPotentialEnergy()
delta = alchemical_potential - reference_potential
# Make sure all kernels are compiled.
reference_integrator.step(1)
alchemical_integrator.step(1)
# Time simulations.
logger.info("Simulating reference system...")
initial_time = time.time()
reference_integrator.step(nsteps)
reference_state = reference_context.getState(getEnergy=True)
reference_potential = reference_state.getPotentialEnergy()
final_time = time.time()
reference_time = final_time - initial_time
logger.info("Simulating alchemical system...")
initial_time = time.time()
alchemical_integrator.step(nsteps)
alchemical_state = alchemical_context.getState(getEnergy=True)
alchemical_potential = alchemical_state.getPotentialEnergy()
final_time = time.time()
alchemical_time = final_time - initial_time
logger.info("TIMINGS")
logger.info("reference system : %12.3f s for %8d steps (%12.3f ms/step)" % (reference_time, nsteps, reference_time/nsteps*1000))
logger.info("alchemical system : %12.3f s for %8d steps (%12.3f ms/step)" % (alchemical_time, nsteps, alchemical_time/nsteps*1000))
logger.info("alchemical simulation is %12.3f x slower than unperturbed system" % (alchemical_time / reference_time))
return delta
