def setUp(self):
# Obtain topologies/positions
prmtop = utils.get_data_filename('blues', 'tests/data/TOL-parm.prmtop')
inpcrd = utils.get_data_filename('blues', 'tests/data/TOL-parm.inpcrd')
structure = parmed.load_file(prmtop, xyz=inpcrd)
self.atom_indices = utils.atomIndexfromTop('LIG', structure.topology)
self.functions = { 'lambda_sterics' : 'step(0.199999-lambda) + step(lambda-0.2)*step(0.8-lambda)*abs(lambda-0.5)*1/0.3 + step(lambda-0.800001)',
'lambda_electrostatics' : 'step(0.2-lambda)- 1/0.2*lambda*step(0.2-lambda) + 1/0.2*(lambda-0.8)*step(lambda-0.8)' }
self.opt = { 'temperature' : 300.0, 'friction' : 1, 'dt' : 0.002,
'nIter' : 10, 'nstepsNC' : 10, 'nstepsMD' : 50,
'nonbondedMethod' : 'PME', 'nonbondedCutoff': 10, 'constraints': 'HBonds',
'trajectory_interval' : 10, 'reporter_interval' : 10,
'platform' : None, 'outfname' : 'smartdart-test',
'verbose' : False }
#Initialize the SmartDartMove object
self.move = SmartDartMove(structure,
basis_particles=[100, 110, 150],
coord_files = [inpcrd, inpcrd], topology=prmtop,
self_dart=False, resname='LIG', )
self.engine = MoveEngine(self.move)
self.engine.selectMove()
#Initialize the SimulationFactory object
sims = SimulationFactory(structure, self.engine, **self.opt)
system = sims.generateSystem(structure, **self.opt)
alch_system = sims.generateAlchSystem(system, self.atom_indices)
self.nc_sim = sims.generateSimFromStruct(structure, self.engine, alch_system, ncmc=True, **self.opt)
self.initial_positions = self.nc_sim.context.getState(getPositions=True).getPositions(asNumpy=True)
def test_simulationRun(self):
"""Tests the Simulation.runNCMC() function"""
self.opt = { 'temperature' : 300.0, 'friction' : 1, 'dt' : 0.002,
'nIter' : 2, 'nstepsNC' : 100, 'nstepsMD' : 2, 'nprop' : 1,
'nonbondedMethod' : 'NoCutoff', 'constraints': 'HBonds',
'trajectory_interval' : 1, 'reporter_interval' : 1, 'outfname' : 'blues-test',
'platform' : None, 'write_move' : False}
testsystem = testsystems.AlanineDipeptideVacuum(constraints=None)
structure = parmed.openmm.topsystem.load_topology(topology=testsystem.topology,
system=testsystem.system,
xyz=testsystem.positions,
)
self.model = RandomLigandRotationMove(structure, resname='ALA')
self.model.atom_indices = range(22)
self.model.topology = structure.topology
self.model.positions = structure.positions
self.model.calculateProperties()
self.mover = MoveEngine(self.model)
#Initialize the SimulationFactory object
sims = SimulationFactory(structure, self.mover, **self.opt)
#print(sims)
system = sims.generateSystem(structure, **self.opt)
simdict = sims.createSimulationSet()
alch_system = sims.generateAlchSystem(system, self.model.atom_indices)
self.nc_sim = sims.generateSimFromStruct(structure, self.mover, alch_system, ncmc=True, **self.opt)
self.model.calculateProperties()
self.initial_positions = self.nc_sim.context.getState(getPositions=True).getPositions(asNumpy=True)
asim = Simulation(sims, self.mover, **self.opt)
asim.run(self.opt['nIter'])
def test_simulationfactory(self):
#Initialize the SimulationFactory object
move = RandomLigandRotationMove(self.full_struct, 'LIG')
engine = MoveEngine(move)
sims = SimulationFactory(self.full_struct, engine, **self.opt)
system = sims.generateSystem(self.full_struct, **self.opt)
self.assertIsInstance(system, openmm.System)
alch_system = sims.generateAlchSystem(system, move.atom_indices)
self.assertIsInstance(alch_system, openmm.System)
md_sim = sims.generateSimFromStruct(self.full_struct, engine, system, **self.opt)
self.assertIsInstance(md_sim, openmm.app.simulation.Simulation)
nc_sim = sims.generateSimFromStruct(self.full_struct, engine, alch_system, ncmc=True, **self.opt)
self.assertIsInstance(nc_sim, openmm.app.simulation.Simulation)
def setUp(self):
# Obtain topologies/positions
prmtop = testsystems.get_data_filename("data/alanine-dipeptide-gbsa/alanine-dipeptide.prmtop")
inpcrd = testsystems.get_data_filename("data/alanine-dipeptide-gbsa/alanine-dipeptide.crd")
testsystem = testsystems.AlanineDipeptideVacuum(constraints=None)
structure = parmed.openmm.topsystem.load_topology(topology=testsystem.topology,
system=testsystem.system,
xyz=testsystem.positions,
)
#self.atom_indices = utils.atomIndexfromTop('LIG', structure.topology)
self.functions = { 'lambda_sterics' : 'step(0.199999-lambda) + step(lambda-0.2)*step(0.8-lambda)*abs(lambda-0.5)*1/0.3 + step(lambda-0.800001)',
'lambda_electrostatics' : 'step(0.2-lambda)- 1/0.2*lambda*step(0.2-lambda) + 1/0.2*(lambda-0.8)*step(lambda-0.8)' }
self.opt = { 'temperature' : 300.0, 'friction' : 1, 'dt' : 0.002,
'nIter' : 10, 'nstepsNC' : 10, 'nstepsMD' : 50,
'nonbondedMethod' : 'NoCutoff', 'nonbondedCutoff': 10, 'constraints': 'HBonds',
'trajectory_interval' : 10, 'reporter_interval' : 10, 'outfname' : 'smartdart-test',
'platform' : None,
'verbose' : False }
#Initialize the Model object
basis_particles = [0,2,7]
self.move = SmartDartMove(structure, basis_particles=basis_particles,
coord_files=[inpcrd, inpcrd],
topology=prmtop,
resname='ALA', self_dart=True)
self.move.atom_indices = range(22)
self.move.topology = structure.topology
self.move.positions = structure.positions
self.move_engine = MoveEngine(self.move)
#Initialize the SimulationFactory object
sims = SimulationFactory(structure, self.move_engine, **self.opt)
system = sims.generateSystem(structure, **self.opt)
alch_system = sims.generateAlchSystem(system, self.move.atom_indices)
self.nc_sim = sims.generateSimFromStruct(structure, self.move_engine, alch_system, ncmc=True, **self.opt)
self.move.calculateProperties()
self.initial_positions = self.nc_sim.context.getState(getPositions=True).getPositions(asNumpy=True)
def test_simulationRun(self):
"""Tests the Simulation.runMC() function"""
self.opt = {
'temperature': 300.0,
'friction': 1,
'dt': 0.00002,
'nIter': 2,
'nstepsNC': 2,
'nstepsMD': 1,
'nprop': 1,
'nonbondedMethod': 'NoCutoff',
'constraints': 'HBonds',
'trajectory_interval': 1,
'reporter_interval': 1,
'outfname': 'mc-test',
'platform': None,
'constraints': 'HBonds',
'mc_per_iter': 2
}
structure = self.full_struct
class SetRotationMove(RandomLigandRotationMove):
def __init__(self, structure, resname='LIG'):
super(SetRotationMove, self).__init__(structure, resname)
def move(self, context):
"""Function that performs a random rotation about the
center of mass of the ligand.
"""
#TODO: check if we need to deepcopy
positions = context.getState(getPositions=True).getPositions(
asNumpy=True)
self.positions = positions[self.atom_indices]
self.center_of_mass = self.getCenterOfMass(
self.positions, self.masses)
reduced_pos = self.positions - self.center_of_mass
# Define random rotational move on the ligand
#set rotation so that test is reproducible
set_rotation_matrix = np.array(
[[-0.62297988, -0.17349253, 0.7627558],
[0.55082352, -0.78964857, 0.27027502],
[0.55541834, 0.58851973, 0.58749893]])
#set_rotation_matrix = np.array([[1, 0, 0],
# [0, 1, 0],
# [0, 0, 1]])
#multiply lig coordinates by rot matrix and add back COM translation from origin
rot_move = np.dot(reduced_pos, set_rotation_matrix
) * positions.unit + self.center_of_mass
# Update ligand positions in nc_sim
for index, atomidx in enumerate(self.atom_indices):
positions[atomidx] = rot_move[index]
context.setPositions(positions)
positions = context.getState(getPositions=True).getPositions(
asNumpy=True)
self.positions = positions[self.atom_indices]
return context
self.model = SetRotationMove(structure, resname='ALA')
#self.model = RandomLigandRotationMove(structure, resname='ALA')
self.model.atom_indices = range(22)
self.model.topology = structure[self.model.atom_indices].topology
self.model.positions = structure[self.model.atom_indices].positions
self.model.calculateProperties()
self.mover = MoveEngine(self.model)
#Initialize the SimulationFactory object
sims = SimulationFactory(structure, self.mover, **self.opt)
#print(sims)
system = sims.generateSystem(structure, **self.opt)
simdict = sims.createSimulationSet()
alch_system = sims.generateAlchSystem(system, self.model.atom_indices)
self.nc_sim = sims.generateSimFromStruct(structure,
self.mover,
alch_system,
ncmc=True,
**self.opt)
self.model.calculateProperties()
self.initial_positions = self.nc_sim.context.getState(
getPositions=True).getPositions(asNumpy=True)
mc_sim = Simulation(sims, self.mover, **self.opt)
#monkeypatch to access acceptance value
def nacceptRejectMC(self, temperature=300, **opt):
"""Function that chooses to accept or reject the proposed move.
"""
md_state0 = self.current_state['md']['state0']
md_state1 = self.current_state['md']['state1']
log_mc = (md_state1['potential_energy'] -
md_state0['potential_energy']) * (
-1.0 / self.nc_sim.context._integrator.kT)
randnum = math.log(np.random.random())
if log_mc > randnum:
self.accept += 1
print('MC MOVE ACCEPTED: log_mc {} > randnum {}'.format(
log_mc, randnum))
self.md_sim.context.setPositions(md_state1['positions'])
else:
self.reject += 1
print('MC MOVE REJECTED: log_mc {} < {}'.format(
log_mc, randnum))
self.md_sim.context.setPositions(md_state0['positions'])
self.log_mc = log_mc
self.md_sim.context.setVelocitiesToTemperature(
self.opt['temperature'])
mc_sim.acceptRejectMC = nacceptRejectMC
nacceptRejectMC.__get__(mc_sim)
mc_sim.acceptRejectMC = types.MethodType(nacceptRejectMC, mc_sim)
mc_sim.runMC(self.opt['nIter'])
#get log acceptance
print(mc_sim.log_mc)
#if mc is working, should be around -24.1
assert mc_sim.log_mc <= -23.8 and mc_sim.log_mc >= -24.3
