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 ligrot_example(yaml_file):
# Parse a YAML configuration, return as Dict
cfg = Settings(yaml_file).asDict()
structure = cfg['Structure']
#Select move type
ligand = RandomLigandRotationMove(structure, 'LIG')
#Iniitialize object that selects movestep
ligand_mover = MoveEngine(ligand)
#Generate the openmm.Systems outside SimulationFactory to allow modifications
systems = SystemFactory(structure, ligand.atom_indices, cfg['system'])
#Freeze atoms in the alchemical system to speed up alchemical calculation
systems.alch = systems.freeze_radius(structure, systems.alch, **cfg['freeze'])
#Generate the OpenMM Simulations
simulations = SimulationFactory(systems, ligand_mover, cfg['simulation'], cfg['md_reporters'],
cfg['ncmc_reporters'])
# Run BLUES Simulation
blues = BLUESSimulation(simulations, cfg['simulation'])
blues.run()
from blues.moves import WaterTranslationMove, MoveEngine
from blues.simulation import *
import json
from blues.settings import Settings
# Parse a YAML configuration, return as Dict
opt = Settings('water_cuda.yaml').asDict()
structure = opt['Structure']
print(json.dumps(opt, sort_keys=True, indent=2, skipkeys=True, default=str))
# Select move type
water = WaterTranslationMove(structure,
water_name='WAT',
protein_selection='index 9',
radius=2 * unit.nanometers)
# Initialize object that selects movestep
water_mover = MoveEngine(water)
#Generate the openmm.Systems outside SimulationFactory to allow modifications
systems = SystemFactory(structure, water.atom_indices, opt['system'])
# Restrain atoms in the MD and alchemical system
systems.md = systems.restrain_positions(structure, systems.md,
**opt['restraints'])
systems.alch = systems.restrain_positions(structure, systems.alch,
**opt['restraints'])
# Generate the OpenMM Simulations
simulations = SimulationFactory(systems, water_mover, opt['simulation'],
opt['md_reporters'], opt['ncmc_reporters'])
from WaterTranslation import WaterTranslation
from blues.moves import MoveEngine
from blues.simulation import *
import json
from blues.settings import Settings
opt = Settings('example.yaml').asDict()
structure = opt['Structure']
#restart = parmed.amber.Rst7('NPT_MD.rst7')
#structure.positions = restart.positions
#structure.box = restart.box
print(json.dumps(opt, sort_keys=True, indent=2, skipkeys=True, default=str))
#Select move type
ligand = WaterTranslationMove(structure, water_name='WAT')
#Iniitialize object that selects movestep
ligand_mover = MoveEngine(ligand)
#Generate the openmm.Systems outside SimulationFactory to allow modifications
systems = SystemFactory(structure, ligand.atom_indices, opt['system'])
# Uncomment this section freeze atoms in the system
# Used for MD or BLUES production runs of the C60 buckyball and the water box with dividing graphene sheets
#systems.md = systems.freeze_atoms(structure, systems.md, **opt['freeze'])
#systems.alch = systems.freeze_atoms(structure, systems.alch, **opt['freeze'])
# Uncomment this section to restrain atoms in the MD and alchemical system
# Used for MD and BLUES production runs of MUP-1 and HSP90 protein-ligand systems to restrain all of the alpha carbons and the ligands
#systems.md = systems.restrain_positions(structure, systems.md, **opt['restraints'])
#systems.alch = systems.restrain_positions(structure, systems.alch, **opt['restraints'])
def test_blues_simulationRunYAML(self):
yaml_cfg = """
output_dir: .
outfname: ala-dipep-vac
logger:
level: info
stream: True
system:
nonbonded: NoCutoff
constraints: HBonds
simulation:
dt: 0.002 * picoseconds
friction: 1 * 1/picoseconds
temperature: 400 * kelvin
nIter: 1
nstepsMD: 4
nstepsNC: 4
md_reporters:
stream:
title: md
reportInterval: 1
totalSteps: 4 # nIter * nstepsMD
step: True
speed: True
progress: True
remainingTime: True
currentIter : True
ncmc_reporters:
stream:
title: ncmc
reportInterval: 1
totalSteps: 4 # Use nstepsNC
step: True
speed: True
progress: True
remainingTime: True
protocolWork : True
alchemicalLambda : True
currentIter : True
"""
print('Testing Simulation.run() from YAML')
yaml_cfg = Settings(yaml_cfg)
cfg = yaml_cfg.asDict()
simulations = SimulationFactory(self.systems, self.engine,
cfg['simulation'], cfg['md_reporters'],
cfg['ncmc_reporters'])
blues = BLUESSimulation(simulations)
before_iter = blues._md_sim.context.getState(
getPositions=True).getPositions(asNumpy=True)
blues.run()
after_iter = blues._md_sim.context.getState(
getPositions=True).getPositions(asNumpy=True)
#Check that our system has run dynamics
pos_compare = np.not_equal(before_iter, after_iter).all()
self.assertTrue(pos_compare)
os.remove('ala-dipep-vac.log')
from mup_WaterTranslationRotation import WaterTranslationRotationMove
from blues.moves import MoveEngine
from blues.simulation import *
import json
from blues.settings import Settings
opt = Settings('mup.yaml').asDict()
structure = opt['Structure']
restart = parmed.amber.Rst7(
'/oasis/tscc/scratch/bergazin/water/mup_NPT_MD.rst7'
) #change to dir where rst is
#restart = parmed.amber.Rst7('/oasis/tscc/scratch/bergazin/water/MUP-1/NCMCsteps_variation_trials/1000_NCMCsteps_trials/t1/t1.rst7')
structure.positions = restart.positions
#structure.velocities = restart.velocities
structure.box = restart.box
print("structure.box", structure.box)
print(json.dumps(opt, sort_keys=True, indent=2, skipkeys=True, default=str))
#Select move type
ligand = WaterTranslationRotationMove(structure, water_name='WAT')
#Iniitialize object that selects movestep
ligand_mover = MoveEngine(ligand)
#Generate the openmm.Systems outside SimulationFactory to allow modifications
systems = SystemFactory(structure, ligand.atom_indices, opt['system'])
#Freeze atoms in the alchemical system
#systems.md = systems.freeze_atoms(structure, systems.md, **opt['freeze'])
#systems.alch = systems.freeze_atoms(structure, systems.alch, **opt['freeze'])
def test_blues_simulationRunYAML(self, tmpdir, structure, tol_atom_indices, system_cfg, engine):
yaml_cfg = """
output_dir: .
outfname: tol-test
logger:
level: info
stream: True
system:
nonbondedMethod: PME
nonbondedCutoff: 8.0 * angstroms
constraints: HBonds
simulation:
dt: 0.002 * picoseconds
friction: 1 * 1/picoseconds
temperature: 300 * kelvin
nIter: 1
nstepsMD: 2
nstepsNC: 2
platform: CPU
md_reporters:
stream:
title: md
reportInterval: 1
totalSteps: 2 # nIter * nstepsMD
step: True
speed: True
progress: True
remainingTime: True
currentIter : True
ncmc_reporters:
stream:
title: ncmc
reportInterval: 1
totalSteps: 2 # Use nstepsNC
step: True
speed: True
progress: True
remainingTime: True
protocolWork : True
alchemicalLambda : True
currentIter : True
"""
print('Testing Simulation.run() from YAML')
yaml_cfg = Settings(yaml_cfg)
cfg = yaml_cfg.asDict()
cfg['output_dir'] = tmpdir
# os.getenv is equivalent, and can also give a default value instead of `None`
PLATFORM = os.getenv('OMM_PLATFORM', 'CPU')
cfg['simulation']['platform'] = PLATFORM
systems = SystemFactory(structure, tol_atom_indices, cfg['system'])
simulations = SimulationFactory(systems, engine, cfg['simulation'], cfg['md_reporters'], cfg['ncmc_reporters'])
blues = BLUESSimulation(simulations)
blues._md_sim.minimizeEnergy()
blues._alch_sim.minimizeEnergy()
blues._ncmc_sim.minimizeEnergy()
before_iter = blues._md_sim.context.getState(getPositions=True).getPositions(asNumpy=True)
blues.run()
after_iter = blues._md_sim.context.getState(getPositions=True).getPositions(asNumpy=True)
#Check that our system has run dynamics
pos_compare = np.not_equal(before_iter, after_iter).all()
assert pos_compare
def test_blues_simulationRunYAML(self, tmpdir, structure, tol_atom_indices,
system_cfg, engine):
yaml_cfg = """
output_dir: .
outfname: tol-test
logger:
level: info
stream: True
system:
nonbondedMethod: PME
nonbondedCutoff: 8.0 * angstroms
constraints: HBonds
simulation:
dt: 0.002 * picoseconds
friction: 1 * 1/picoseconds
temperature: 300 * kelvin
nIter: 1
nstepsMD: 2
nstepsNC: 2
platform: CPU
md_reporters:
stream:
title: md
reportInterval: 1
totalSteps: 2 # nIter * nstepsMD
step: True
speed: True
progress: True
remainingTime: True
currentIter : True
ncmc_reporters:
stream:
title: ncmc
reportInterval: 1
totalSteps: 2 # Use nstepsNC
step: True
speed: True
progress: True
remainingTime: True
protocolWork : True
alchemicalLambda : True
currentIter : True
"""
print('Testing Simulation.run() from YAML')
yaml_cfg = Settings(yaml_cfg)
cfg = yaml_cfg.asDict()
cfg['output_dir'] = tmpdir
# os.getenv is equivalent, and can also give a default value instead of `None`
PLATFORM = os.getenv('OMM_PLATFORM', 'CPU')
cfg['simulation']['platform'] = PLATFORM
systems = SystemFactory(structure, tol_atom_indices, cfg['system'])
simulations = SimulationFactory(systems, engine, cfg['simulation'],
cfg['md_reporters'],
cfg['ncmc_reporters'])
blues = BLUESSimulation(simulations)
blues._md_sim.minimizeEnergy()
blues._alch_sim.minimizeEnergy()
blues._ncmc_sim.minimizeEnergy()
before_iter = blues._md_sim.context.getState(
getPositions=True).getPositions(asNumpy=True)
blues.run()
after_iter = blues._md_sim.context.getState(
getPositions=True).getPositions(asNumpy=True)
#Check that our system has run dynamics
pos_compare = np.not_equal(before_iter, after_iter).all()
assert pos_compare
from WaterTranslation import WaterTranslation
from blues.moves import MoveEngine
from blues.simulation import *
import json
from blues.settings import Settings
opt = Settings('equilibration.yaml').asDict()
structure = opt['Structure']
#restart = parmed.amber.Rst7('NPT_MD.rst7')
structure.positions = restart.positions
structure.box = restart.box
print(json.dumps(opt, sort_keys=True, indent=2, skipkeys=True, default=str))
#Select move type
ligand = WaterTranslationMove(structure, water_name='WAT')
#Iniitialize object that selects movestep
ligand_mover = MoveEngine(ligand)
#Generate the openmm.Systems outside SimulationFactory to allow modifications
systems = SystemFactory(structure, ligand.atom_indices, opt['system'])
# Uncomment this section freeze atoms in the system
# Used for MD or BLUES production runs of the C60 buckyball and the water box with dividing graphene sheets
#systems.md = systems.freeze_atoms(structure, systems.md, **opt['freeze'])
#systems.alch = systems.freeze_atoms(structure, systems.alch, **opt['freeze'])
# Uncomment this section to restrain atoms in the MD and alchemical system
# Used for MD and BLUES production runs of MUP-1 and HSP90 protein-ligand systems to restrain all of the alpha carbons and the ligands
#systems.md = systems.restrain_positions(structure, systems.md, **opt['restraints'])