def overlap_check():
"""
BUGS TO REPORT:
* Even if epsilon = 0, energy of two overlapping atoms is 'nan'.
* Periodicity in 'nan' if dr = 0.1 even in nonperiodic system
"""
# Create a reference system.
logger.info("Creating Lennard-Jones cluster system...")
#[reference_system, positions] = testsystems.LennardJonesFluid()
#receptor_atoms = [0]
#ligand_atoms = [1]
system_container = testsystems.LysozymeImplicit()
(reference_system, positions) = system_container.system, system_container.positions
receptor_atoms = range(0,2603) # T4 lysozyme L99A
ligand_atoms = range(2603,2621) # p-xylene
unit = positions.unit
positions = units.Quantity(np.array(positions / unit), unit)
factory = AbsoluteAlchemicalFactory(reference_system, ligand_atoms=ligand_atoms)
alchemical_state = AlchemicalState(0.00, 0.00, 0.00, 1.0)
# Create the perturbed system.
logger.info("Creating alchemically-modified state...")
alchemical_system = factory.createPerturbedSystem(alchemical_state)
# Compare energies.
timestep = 1.0 * units.femtosecond
logger.info("Computing reference energies...")
integrator = openmm.VerletIntegrator(timestep)
context = openmm.Context(reference_system, integrator)
context.setPositions(positions)
state = context.getState(getEnergy=True)
reference_potential = state.getPotentialEnergy()
del state, context, integrator
logger.info(reference_potential)
logger.info("Computing alchemical energies...")
integrator = openmm.VerletIntegrator(timestep)
context = openmm.Context(alchemical_system, integrator)
dr = 0.1 * units.angstroms # TODO: Why does 0.1 cause periodic 'nan's?
a = receptor_atoms[-1]
b = ligand_atoms[-1]
delta = positions[a,:] - positions[b,:]
for k in range(3):
positions[ligand_atoms,k] += delta[k]
for i in range(30):
r = dr * i
positions[ligand_atoms,0] += dr
context.setPositions(positions)
state = context.getState(getEnergy=True)
alchemical_potential = state.getPotentialEnergy()
logger.info("%8.3f A : %f " % (r / units.angstroms, alchemical_potential / units.kilocalories_per_mole))
del state, context, integrator
return
def tooslow_obcgbsa_complex():
# This test is too slow for travis-ci.
logger.info("Creating T4 lysozyme system...")
system_container = testsystems.LysozymeImplicit()
(reference_system, positions) = system_container.system, system_container.positions
receptor_atoms = range(0,2603) # T4 lysozyme L99A
ligand_atoms = range(2603,2621) # p-xylene
alchemical_factory_check(reference_system, positions, receptor_atoms, ligand_atoms)
#benchmark(reference_system, positions, receptor_atoms, ligand_atoms)
logger.info("")