def sidechain_example(yaml_file):
# Parse a YAML configuration, return as Dict
cfg = Settings(yaml_file).asDict()
structure = cfg['Structure']
#Select move type
sidechain = SideChainMove(structure, [1])
#Iniitialize object that selects movestep
sidechain_mover = MoveEngine(sidechain)
#Generate the openmm.Systems outside SimulationFactory to allow modifications
systems = SystemFactory(structure, sidechain.atom_indices, cfg['system'])
#Generate the OpenMM Simulations
simulations = SimulationFactory(systems, sidechain_mover, cfg['simulation'], cfg['md_reporters'],
cfg['ncmc_reporters'])
# Run BLUES Simulation
blues = BLUESSimulation(simulations, cfg['simulation'])
blues.run()
#Analysis
import mdtraj as md
import numpy as np
traj = md.load_netcdf('vacDivaline-test/vacDivaline.nc', top='tests/data/vacDivaline.prmtop')
indicies = np.array([[0, 4, 6, 8]])
dihedraldata = md.compute_dihedrals(traj, indicies)
with open("vacDivaline-test/dihedrals.txt", 'w') as output:
for value in dihedraldata:
output.write("%s\n" % str(value)[1:-1])
def runNCMC(platform_name, relaxstepsNC, themdsteps):
#Define some options
opt = {
'temperature': 300.0,
'friction': 1,
'dt': 0.002,
'nIter': 50000,
'nstepsNC': relaxstepsNC,
'nstepsMD': themdsteps,
'nonbondedMethod': 'PME',
'nonbondedCutoff': 10,
'constraints': 'HBonds',
'trajectory_interval': 1000,
'reporter_interval': 1000,
'platform': platform_name,
'verbose': False,
'write_ncmc': False
}
#Generate the ParmEd Structure
#prmtop = utils.get_data_filename('blues', 'tests/data/eqToluene.prmtop')#
#inpcrd = utils.get_data_filename('blues', 'tests/data/eqToluene.inpcrd')
prmtop = '/home/burleyk/projects/sidechain/inputs/watDivaline.prmtop'
inpcrd = '/home/burleyk/projects/sidechain/inputs/watDivaline.inpcrd'
struct = parmed.load_file(prmtop, xyz=inpcrd)
#Define the 'model' object we are perturbing here.
# Calculate particle masses of object to be moved
ligand = SideChainMove(struct, [1])
ligand.atom_indices = ligand.rot_bond_atoms
# Initialize object that proposes moves.
ligand_mover = MoveEngine(ligand)
# Generate the MD, NCMC, ALCHEMICAL Simulation objects
simulations = SimulationFactory(struct, ligand_mover, **opt)
simulations.createSimulationSet()
blues = Simulation(simulations, ligand_mover, **opt)
#add the reporter here
blues.md_sim.reporters.append(
openmm.app.dcdreporter.DCDReporter('accept.dcd', 1000))
blues.runNCMC()
def setUp(self):
# Obtain topologies/positions
prmtop = utils.get_data_filename('blues', 'tests/data/vacDivaline.prmtop')
inpcrd = utils.get_data_filename('blues', 'tests/data/vacDivaline.inpcrd')
self.struct = 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, 'outfname' : 'vacDivaline',
'platform' : None,
'verbose' : False }
self.sidechain = SideChainMove(self.struct, [1])
self.mover = MoveEngine(self.sidechain)
class SideChainTester(unittest.TestCase):
"""
Test the SmartDartMove.move() function.
"""
def setUp(self):
# Obtain topologies/positions
prmtop = utils.get_data_filename('blues', 'tests/data/vacDivaline.prmtop')
inpcrd = utils.get_data_filename('blues', 'tests/data/vacDivaline.inpcrd')
self.struct = 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, 'outfname' : 'vacDivaline',
'platform' : None,
'verbose' : False }
self.sidechain = SideChainMove(self.struct, [1])
self.mover = MoveEngine(self.sidechain)
def test_getRotBondAtoms(self):
vals = [v for v in self.sidechain.rot_atoms[1].values()][0]
self.assertEqual(len(vals), 11)
#Ensure it selects 1 rotatable bond in Valine
self.assertEqual(len(self.sidechain.rot_bonds), 1)
def test_sidechain_move(self):
simulations = SimulationFactory(self.struct, self.mover, **self.opt)
simulations.createSimulationSet()
nc_context = simulations.nc.context
self.sidechain.move(nc_context, verbose=False)
def setUp(self):
# Obtain topologies/positions
prmtop = utils.get_data_filename('blues',
'tests/data/vacDivaline.prmtop')
inpcrd = utils.get_data_filename('blues',
'tests/data/vacDivaline.inpcrd')
self.struct = parmed.load_file(prmtop, xyz=inpcrd)
self.sidechain = SideChainMove(self.struct, [1])
self.engine = MoveEngine(self.sidechain)
self.engine.selectMove()
self.system_cfg = {
'nonbondedMethod': app.NoCutoff,
'constraints': app.HBonds
}
self.systems = SystemFactory(self.struct, self.sidechain.atom_indices,
self.system_cfg)
self.cfg = {
'dt': 0.002 * unit.picoseconds,
'friction': 1 * 1 / unit.picoseconds,
'temperature': 300 * unit.kelvin,
'nIter': 1,
'nstepsMD': 1,
'nstepsNC': 4,
'alchemical_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.simulations = SimulationFactory(self.systems, self.engine,
self.cfg)
from blues.moves import SideChainMove
from blues.moves import MoveEngine
from blues.simulation import *
import json
from blues.settings import *
from blues.simulation import *
import json
from blues.settings import *
# Parse a YAML configuration, return as Dict
cfg = Settings('sidechain_cudayaml').asDict()
structure = cfg['Structure']
#Select move type
sidechain = SideChainMove(structure, [1])
#Iniitialize object that selects movestep
sidechain_mover = MoveEngine(sidechain)
#Generate the openmm.Systems outside SimulationFactory to allow modifications
systems = SystemFactory(structure, sidechain.atom_indices, cfg['system'])
#Generate the OpenMM Simulations
simulations = SimulationFactory(systems, sidechain_mover, cfg['simulation'],
cfg['md_reporters'], cfg['ncmc_reporters'])
# Run BLUES Simulation
blues = BLUESSimulation(simulations, cfg['simulation'])
blues.run()
#Analysis
import mdtraj as md
def runNCMC(platform_name, nstepsNC, nprop, outfname):
#Generate the ParmEd Structure
prmtop = utils.get_data_filename('blues', 'tests/data/vacDivaline.prmtop')
inpcrd = utils.get_data_filename('blues', 'tests/data/vacDivaline.inpcrd')
struct = parmed.load_file(prmtop, xyz=inpcrd)
print('Structure: %s' % struct.topology)
#Define some options
opt = {
'temperature': 300.0,
'friction': 1,
'dt': 0.004,
'hydrogenMass': 3.024,
'nIter': 100,
'nstepsNC': nstepsNC,
'nstepsMD': 1000,
'nprop': nprop,
'nonbondedMethod': 'PME',
'nonbondedCutoff': 10,
'constraints': 'HBonds',
'trajectory_interval': 100,
'reporter_interval': 250,
'ncmc_traj': None,
'write_move': False,
'platform': platform_name,
'outfname': 'vacDivaline',
'verbose': False
}
#Define the 'model' object we are perturbing here.
# Calculate particle masses of object to be moved
ligand = SideChainMove(struct, [1])
# Initialize object that proposes moves.
ligand_mover = MoveEngine(ligand)
# Generate the MD, NCMC, ALCHEMICAL Simulation objects
simulations = SimulationFactory(struct, ligand_mover, **opt)
simulations.createSimulationSet()
# Add reporters to MD simulation.
trajfile = outfname + '-nc{}.dcd'.format(nstepsNC)
traj_reporter = openmm.app.DCDReporter(trajfile,
opt['trajectory_interval'])
progress_reporter = openmm.app.StateDataReporter(
sys.stdout,
separator="\t",
reportInterval=opt['reporter_interval'],
step=True,
totalSteps=opt['nIter'] * opt['nstepsMD'],
time=True,
speed=True,
progress=True,
elapsedTime=True,
remainingTime=True)
simulations.md.reporters.append(traj_reporter)
simulations.md.reporters.append(progress_reporter)
# Run BLUES Simulation
blues = Simulation(simulations, ligand_mover, **opt)
blues.run(opt['nIter'])
#Analysis
import mdtraj as md
import numpy as np
traj = md.load_dcd(trajfile, top='protein.pdb')
indicies = np.array([[0, 4, 6, 8]])
dihedraldata = md.compute_dihedrals(traj, indicies)
with open("dihedrals-%iNC.txt" % (nstepsNC), 'w') as output:
for value in dihedraldata:
output.write("%s\n" % str(value)[1:-1])