def test_xtc_reporter_append(tmpdir, get_fn):
pdb = PDBFile(get_fn('native.pdb'))
forcefield = ForceField('amber99sbildn.xml', 'amber99_obc.xml')
# NO PERIODIC BOUNDARY CONDITIONS
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=CutoffNonPeriodic,
nonbondedCutoff=1.0 * nanometers,
constraints=HBonds,
rigidWater=True)
integrator = LangevinIntegrator(300 * kelvin, 1.0 / picoseconds,
2.0 * femtoseconds)
integrator.setConstraintTolerance(0.00001)
platform = Platform.getPlatformByName('Reference')
simulation = Simulation(pdb.topology, system, integrator, platform)
simulation.context.setPositions(pdb.positions)
simulation.context.setVelocitiesToTemperature(300 * kelvin)
tmpdir = str(tmpdir)
xtcfile = os.path.join(tmpdir, 'traj.xtc')
xtcfile_cp = os.path.join(tmpdir, 'traj_cp.xtc')
checkpoint = os.path.join(tmpdir, 'checkpoint.chk')
reporter = XTCReporter(xtcfile, 2)
simulation.reporters.append(reporter)
simulation.reporters.append(CheckpointReporter(checkpoint, 10))
simulation.step(10)
reporter.close()
shutil.copyfile(xtcfile, xtcfile_cp)
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=CutoffNonPeriodic,
nonbondedCutoff=1.0 * nanometers,
constraints=HBonds,
rigidWater=True)
integrator = LangevinIntegrator(300 * kelvin, 1.0 / picoseconds,
2.0 * femtoseconds)
integrator.setConstraintTolerance(0.00001)
platform = Platform.getPlatformByName('Reference')
simulation = Simulation(pdb.topology, system, integrator, platform)
simulation.loadCheckpoint(checkpoint)
reporter = XTCReporter(xtcfile, 2, append=True)
simulation.reporters.append(reporter)
simulation.step(10)
reporter.close()
xtc_traj = md.load(xtcfile, top=get_fn('native.pdb'))
xtc_traj_cp = md.load(xtcfile_cp, top=get_fn('native.pdb'))
eq(xtc_traj.xyz[:5], xtc_traj_cp.xyz)
eq(xtc_traj.n_frames, 10)
eq(xtc_traj_cp.n_frames, 5)
eq(xtc_traj.time[:5], xtc_traj_cp.time)
def _calc_energy(self, coords):
"""
Given some coords, it calculates periodic torsion contribution
to the energy, according to OpenMM.
Parameters
----------
coords : a simtk.unit.Quantity object
The coordinates of a certain conformation of the molecule
Returns
-------
omm_energy : a simtk.unit.Quantity
The dihedral energy from OpenMM
"""
from simtk.openmm import app, LangevinIntegrator, unit
omm_idx_to_force = {}
for idx, force in enumerate(self.omm_system.getForces()):
force.setForceGroup(idx)
omm_idx_to_force[str(type(force).__name__)] = idx
omm_integrator = LangevinIntegrator(300 * unit.kelvin,
1 / unit.picosecond,
0.002 * unit.picoseconds)
omm_simulation = app.Simulation(self.omm_top, self.omm_system,
omm_integrator)
omm_simulation.context.setPositions(coords)
omm_energy = omm_simulation.context.getState(
getEnergy=True, groups={omm_idx_to_force['PeriodicTorsionForce']
}).getPotentialEnergy()
return omm_energy
def energy_minimization(item, platform_name='CUDA', verbose=True):
from simtk.openmm import LangevinIntegrator, Platform, Context, LocalEnergyMinimizer_minimize
from simtk import unit
# Integrator.
integrator = LangevinIntegrator(0 * unit.kelvin, 1.0 / unit.picoseconds,
2.0 * unit.femtoseconds)
# Platform.
platform = Platform.getPlatformByName(platform_name)
# Context.
context = Context(item.system, integrator, platform)
context.setPositions(item.coordinates)
# Minimization.
if verbose == True:
energy = context.getState(getEnergy=True).getPotentialEnergy()
print('Potential energy before minimization: {}'.format(energy))
LocalEnergyMinimizer_minimize(context)
if verbose == True:
energy = context.getState(getEnergy=True).getPotentialEnergy()
print('Potential energy after minimization: {}'.format(energy))
item.coordinates = context.getState(getPositions=True).getPositions(
asNumpy=True)
pass
def _initialize(self):
# Create an integrator
integrator_name = 'Langevin'
if integrator_name == 'GHMC':
from openmmtools.integrators import GHMCIntegrator
self.integrator = GHMCIntegrator(
temperature=self.thermodynamic_state.temperature,
collision_rate=self.collision_rate,
timestep=self.timestep)
elif integrator_name == 'Langevin':
from simtk.openmm import LangevinIntegrator
self.integrator = LangevinIntegrator(
self.thermodynamic_state.temperature, self.collision_rate,
self.timestep)
else:
raise Exception("integrator_name '%s' not valid." %
(integrator_name))
# Create a Context
if self.platform is not None:
self.context = openmm.Context(self.thermodynamic_state.system,
self.integrator, self.platform)
else:
self.context = openmm.Context(self.thermodynamic_state.system,
self.integrator)
self.thermodynamic_state.update_context(self.context, self.integrator)
self.sampler_state.update_context(self.context)
self.context.setVelocitiesToTemperature(
self.thermodynamic_state.temperature)
self._initialized = True
def get_potential_energy(item, coordinates=None, platform_name='CUDA'):
from simtk.openmm import LangevinIntegrator, Platform, Context
from simtk import unit
import numpy as np
integrator = LangevinIntegrator(0.0 * unit.kelvin, 0.0 / unit.picoseconds,
2.0 * unit.femtoseconds)
platform = Platform.getPlatformByName(platform_name)
context = Context(item.system, integrator, platform)
if coordinates is None:
context.setPositions(item.coordinates)
else:
context.setPositions(coordinates)
if item.box is not None:
context.setPeriodicBoxVectors(item.box[0], item.box[1], item.box[2])
state = context.getState(getEnergy=True)
potential_energy = state.getPotentialEnergy()
return potential_energy
def _prep_sim(self, coords, external_forces=[]):
try:
from simtk.openmm import Platform, LangevinIntegrator, Vec3
from simtk.openmm.app import Modeller, ForceField, \
CutoffNonPeriodic, PME, Simulation, HBonds
from simtk.unit import angstrom, nanometers, picosecond, \
kelvin, Quantity, molar
except ImportError:
raise ImportError(
'Please install PDBFixer and OpenMM in order to use ClustENM.')
positions = Quantity([Vec3(*xyz) for xyz in coords], angstrom)
modeller = Modeller(self._topology, positions)
if self._sol == 'imp':
forcefield = ForceField(*self._force_field)
system = forcefield.createSystem(modeller.topology,
nonbondedMethod=CutoffNonPeriodic,
nonbondedCutoff=1.0 * nanometers,
constraints=HBonds)
if self._sol == 'exp':
forcefield = ForceField(*self._force_field)
modeller.addSolvent(forcefield,
padding=self._padding * nanometers,
ionicStrength=self._ionicStrength * molar)
system = forcefield.createSystem(modeller.topology,
nonbondedMethod=PME,
nonbondedCutoff=1.0 * nanometers,
constraints=HBonds)
for force in external_forces:
system.addForce(force)
integrator = LangevinIntegrator(self._temp * kelvin, 1 / picosecond,
0.002 * picosecond)
# precision could be mixed, but single is okay.
platform = self._platform if self._platform is None else Platform.getPlatformByName(
self._platform)
properties = None
if self._platform is None:
properties = {'Precision': 'single'}
elif self._platform in ['CUDA', 'OpenCL']:
properties = {'Precision': 'single'}
simulation = Simulation(modeller.topology, system, integrator,
platform, properties)
simulation.context.setPositions(modeller.positions)
return simulation
def minimise_energy_all_confs(mol, models = None, epsilon = 4, allow_undefined_stereo = True, **kwargs ):
from simtk import unit
from simtk.openmm import LangevinIntegrator
from simtk.openmm.app import Simulation, HBonds, NoCutoff
from rdkit import Chem
from rdkit.Geometry import Point3D
import mlddec
import copy
import tqdm
mol = Chem.AddHs(mol, addCoords = True)
if models is None:
models = mlddec.load_models(epsilon)
charges = mlddec.get_charges(mol, models)
from openforcefield.utils.toolkits import RDKitToolkitWrapper, ToolkitRegistry
from openforcefield.topology import Molecule, Topology
from openforcefield.typing.engines.smirnoff import ForceField
# from openforcefield.typing.engines.smirnoff.forcefield import PME
import parmed
import numpy as np
forcefield = ForceField(get_data_filename("modified_smirnoff99Frosst.offxml")) #FIXME better way of identifying file location
tmp = copy.deepcopy(mol)
tmp.RemoveAllConformers() #XXX workround for speed beacuse seemingly openforcefield records all conformer informations, which takes a long time. but I think this is a ill-practice
molecule = Molecule.from_rdkit(tmp, allow_undefined_stereo = allow_undefined_stereo)
molecule.partial_charges = unit.Quantity(np.array(charges), unit.elementary_charge)
topology = Topology.from_molecules(molecule)
openmm_system = forcefield.create_openmm_system(topology, charge_from_molecules= [molecule])
structure = parmed.openmm.topsystem.load_topology(topology.to_openmm(), openmm_system)
system = structure.createSystem(nonbondedMethod=NoCutoff, nonbondedCutoff=1*unit.nanometer, constraints=HBonds)
integrator = LangevinIntegrator(273*unit.kelvin, 1/unit.picosecond, 0.002*unit.picoseconds)
simulation = Simulation(structure.topology, system, integrator)
out_mol = copy.deepcopy(mol)
for i in tqdm.tqdm(range(out_mol.GetNumConformers())):
conf = mol.GetConformer(i)
structure.coordinates = unit.Quantity(np.array([np.array(conf.GetAtomPosition(i)) for i in range(mol.GetNumAtoms())]), unit.angstroms)
simulation.context.setPositions(structure.positions)
simulation.minimizeEnergy()
# simulation.step(1)
coords = simulation.context.getState(getPositions = True).getPositions(asNumpy = True).value_in_unit(unit.angstrom)
conf = out_mol.GetConformer(i)
for j in range(out_mol.GetNumAtoms()):
conf.SetAtomPosition(j, Point3D(*coords[j]))
return out_mol
def __init__(self, topology=None, system=None, pbc=False, platform='CUDA'):
from .md import MD
from .quench import Quench
from .move import Move
from .distance import Distance
from .acceptance import Acceptance
if topology is None:
raise ValueError('topology is needed')
if system is None:
raise ValueError('system is needed')
integrator = LangevinIntegrator(0 * u.kelvin, 1.0 / u.picoseconds,
2.0 * u.femtoseconds)
#integrator.setConstraintTolerance(0.00001)
if platform == 'CUDA':
platform = Platform.getPlatformByName('CUDA')
properties = {'CudaPrecision': 'mixed'}
elif platform == 'CPU':
platform = Platform.getPlatformByName('CPU')
properties = {}
self.topology = topology
self.context = Context(system, integrator, platform, properties)
self.n_atoms = msm.get(self.context, target='system', n_atoms=True)
self.n_dof = 0
for i in range(system.getNumParticles()):
if system.getParticleMass(i) > 0 * u.dalton:
self.n_dof += 3
for i in range(system.getNumConstraints()):
p1, p2, distance = system.getConstraintParameters(i)
if system.getParticleMass(
p1) > 0 * u.dalton or system.getParticleMass(
p2) > 0 * u.dalton:
self.n_dof -= 1
if any(
type(system.getForce(i)) == CMMotionRemover
for i in range(system.getNumForces())):
self.n_dof -= 3
self.pbc = pbc
if self.pbc:
raise NotImplementedError
self.md = MD(self)
self.quench = Quench(self)
self.move = Move(self)
self.distance = Distance(self)
self.acceptance = Acceptance(self)
def _create_integrator(temperature, use_big_timestep, use_bigger_timestep):
if use_big_timestep:
logger.info("Creating integrator with 3.5 fs timestep")
timestep = 3.5 * femtosecond
elif use_bigger_timestep:
logger.info("Creating integrator with 4.5 fs timestep")
timestep = 4.5 * femtosecond
else:
logger.info("Creating integrator with 2.0 fs timestep")
timestep = 2.0 * femtosecond
return LangevinIntegrator(temperature * kelvin, 1.0 / picosecond, timestep)
def _initialize(self):
system = self._explorer.context.getSystem()
platform = self._explorer.context.getPlatform()
properties = {}
if platform.getName() == 'CUDA':
properties['CudaPrecision'] = 'mixed'
self._integrator = LangevinIntegrator(self._temperature,
self._collision_rate,
self._timestep)
self._context = Context(system, self._integrator, platform, properties)
self._initialized = True
def calculate_fragment_energetics(frag_no=1):
"""
* Create an OpenMM system with a fragment.
* Calculate the energy of the system and print.
:param frag_no: The number of the fragment being analysed (used to access files).
"""
os.chdir(f'group2/frag{frag_no}')
# Necessary due to size of calculation
sys.setrecursionlimit(15000)
pdb = PDBFile(f'QUBE_pro_frag{frag_no}.pdb')
forcefield = ForceField(f'QUBE_pro_frag{frag_no}_plus.xml')
system = forcefield.createSystem(
pdb.topology,
nonbondedMethod=NoCutoff,
)
system = apply_opls_combo(system)
with open(f'QUBE_pro_frag{frag_no}_out.xml', 'w') as outfile:
serialized_system = XmlSerializer.serialize(system)
outfile.write(serialized_system)
# Create the integrator to do Langevin dynamics
integrator = LangevinIntegrator(
298.15 * unit.kelvin, # Temperature of heat bath
1.0 / unit.picoseconds, # Friction coefficient
2.0 * unit.femtoseconds, # Time step
)
platform = Platform.getPlatformByName('CPU')
simulation = Simulation(pdb.topology, system, integrator, platform)
simulation.context.setPositions(pdb.positions)
print('energy from openmm library')
print(simulation.context.getState(getEnergy=True).getPotentialEnergy())
structure = parmed.load_file(f'QUBE_pro_frag{frag_no}.pdb')
energy_comps = parmed.openmm.energy_decomposition_system(structure, system)
total_energy = 0.0
for comp in energy_comps:
total_energy += comp[1]
print(*comp)
print(f'Total energy {total_energy: 6.6f}')
def calc_energy(omm_sys, omm_top, coords):
omm_idx_to_force = {}
for idx, force in enumerate(omm_sys.getForces()):
force.setForceGroup(idx)
omm_idx_to_force[idx] = str(type(force).__name__)
omm_integrator = LangevinIntegrator(300*unit.kelvin,
1/unit.picosecond,
0.002*unit.picoseconds)
omm_simulation = app.Simulation(omm_top, omm_sys, omm_integrator)
#simulation.context.setPositions(positions)
omm_simulation.context.setPositions(coords)
for group in omm_idx_to_force.keys():
omm_energy = omm_simulation.context.getState(getEnergy=True,groups={group}).getPotentialEnergy()
print(omm_idx_to_force[group], omm_energy)
omm_energy = omm_simulation.context.getState(getEnergy=True).getPotentialEnergy()
return omm_energy
def __init__(self, pdb_path, offset_size=2):
# OpenMM init
self.pdb_path = pdb_path
self.pdb = PDBFile(self.pdb_path)
self.forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
self.modeller = Modeller(self.pdb.topology, self.pdb.positions)
# Remove any water that might be present in the PDB file
self.modeller.deleteWater()
# Add any hydrogens not present
self.modeller.addHydrogens(self.forcefield)
self.system = self.forcefield.createSystem(self.modeller.topology,
nonbondedMethod=PME,
nonbondedCutoff=1 *
u.nanometer,
constraints=HBonds)
self.integrator = LangevinIntegrator(300 * u.kelvin, 1 / u.picosecond,
0.002 * u.picoseconds)
self.simulation = Simulation(self.modeller.topology, self.system,
self.integrator)
self.pdb_positions = self.modeller.getPositions()
# Initialize bond dictionary and positions for chemcoord
self.cc_bonds = {}
self.offset_size = offset_size
self._init_pdb_bonds()
self.set_cc_positions(self.pdb_positions)
# Perform initial minimization, which updates self.pdb_positions
min_energy, min_positions = self.run_simulation()
# Reset the positions after the minimization
self.set_cc_positions(self.pdb_positions)
self.torsion_indices = self._get_torsion_indices()
self.starting_positions = min_positions
self.starting_torsions = np.array([
self.zmat.loc[self.torsion_indices[:, 0], 'dihedral'],
self.zmat.loc[self.torsion_indices[:, 1], 'dihedral']
]).T
self.seed_offsets()
'nonbondedMethod': app.LJPME,
'nonbondedCutoff': 1 * nanometer
}
membrane_barostat = MonteCarloMembraneBarostat(
1 * bar, 0.0 * bar * nanometer, 308 * kelvin,
MonteCarloMembraneBarostat.XYIsotropic, MonteCarloMembraneBarostat.ZFree,
15)
system_generator = SystemGenerator(
forcefields=['amber/lipid17.xml', 'amber/tip3p_standard.xml'],
small_molecule_forcefield='gaff-2.11',
barostat=membrane_barostat,
forcefield_kwargs=forcefield_kwargs,
periodic_forcefield_kwargs=periodic_forcefield_kwargs)
system = system_generator.create_system(pdb.topology, molecules=molecule)
integrator = LangevinIntegrator(300 * kelvin, 1 / picosecond,
0.002 * picosecond)
platform = Platform.getPlatformByName('CUDA')
simulation = app.Simulation(pdb.topology, system, integrator, platform)
simulation.context.setPositions(pdb.positions)
simulation.loadState('parent.xml')
simulation.reporters.append(
StateDataReporter('seg.nfo',
5000,
step=True,
potentialEnergy=True,
kineticEnergy=True,
temperature=True))
simulation.reporters.append(HDF5Reporter('seg.h5', 10000))
def _create_integrator(self, *args):
from simtk.openmm import LangevinIntegrator
return LangevinIntegrator(self.temperature, self.frictionCoeff,
self.stepSize)
def calculate_protein_energetics():
"""
* Create an OpenMM system using the first fragment.
* Add each fragment into the system.
* Calculate the energy of the system and print.
"""
os.chdir('group2')
# Necessary due to size of calculation
sys.setrecursionlimit(15000)
frag1 = PDBFile('frag1/no_QUP_frag1.pdb')
forcefield = ForceField(
'frag1/QUBE_pro_frag1.xml',
'frag2/QUBE_pro_frag2_plus.xml',
'frag3/QUBE_pro_frag3_plus.xml',
'frag4/QUBE_pro_frag4_plus.xml',
)
modeller = Modeller(frag1.topology, frag1.positions)
frag2 = PDBFile('frag2/no_QUP_frag2.pdb')
modeller.add(frag2.topology, frag2.positions)
frag3 = PDBFile('frag3/no_QUP_frag3.pdb')
modeller.add(frag3.topology, frag3.positions)
frag4 = PDBFile('frag4/no_QUP_frag4.pdb')
modeller.add(frag4.topology, frag4.positions)
system = forcefield.createSystem(
modeller.topology,
nonbondedMethod=NoCutoff,
)
system = apply_opls_combo(system)
integrator = LangevinIntegrator(
298.15 * unit.kelvin, # Temperature of heat bath
1.0 / unit.picoseconds, # Friction coefficient
2.0 * unit.femtoseconds, # Time step
)
platform = Platform.getPlatformByName('CPU')
simulation = Simulation(modeller.topology, system, integrator, platform)
simulation.context.setPositions(modeller.positions)
print('energy from openmm library')
print(simulation.context.getState(getEnergy=True).getPotentialEnergy())
positions = simulation.context.getState(getPositions=True).getPositions()
with open('output.pdb', 'w') as out_file:
PDBFile.writeFile(simulation.topology, positions, out_file)
structure = parmed.load_file('output.pdb')
energy_comps = parmed.openmm.energy_decomposition_system(structure, system)
total_energy = 0.0
for comp in energy_comps:
total_energy += comp[1]
print(*comp)
print(f'Total energy {total_energy: 6.6f}')
def langevin_NVT(item, time = None, saving_timestep = None, integration_timestep= 2*unit.femtoseconds,
friction=1.0/unit.picoseconds, temperature=300.0*unit.kelvin,
initial_coordinates=None, initial_velocities=None, platform_name='CUDA',
reporters=None, tqdm=True):
"""Newtonian classical dynamics of a molecular system with OpenMM.
The trajectory of a newtonian classical dynamics of a molecular system is obtained together with the
values of potential and kinetic energy. This method is nothing but a short cut to run quick
molecular dynamics with the test systems of this library by means of OpenMM.
Parameters
----------
system: simtk.openmm.System
Molecular system as a system class of OpenMM (see: link)
friction: unit.Quantity
Damping parameter of the Langevin dynamics (in units of 1/time).
initial_coordinates: unit.Quantity
Initial coordinates of the system as a numpy array with shape [n_particles, 3] and units of
length. Where 'n_particles' is the number of particles of the system.
initial_velocities: unit.Quantity
Initial velocities of the system as a numpy array with shape [n_particles, 3] and units of
length/time. Where 'n_particles' is the number of particles of the system.
integration_timestep: unit.Quantity
Time step used by the integrator of the equations of motion. The parameter needs to have
units of time.
saving_timestep: unit.Quantity
Time step used to report the output trajectory. The parameter needs to have units of time.
total_time: unit.Quantity
Total runing time of the simulation. The parameter needs to have units of time.
platform_name: str (default: 'CPU')
Platform to run the dynamics: 'CPU', 'OPENCL' or 'CUDA' (according to those options to run
OpenMM, see documentation),
verbose: bool (default: True)
Verbose switcher. The method will print out information if the value is True.
Returns
-------
time: unit.Quantity
Time as numpy array of shape [n_frames] with units of picoseconds.
position: unit.Quantity
Positions of the systems particles in every reported frame as numpy array of shape [n_frames, n_particles, 3] with units of nanometers.
velocity: unit.Quantity
Velocities of the systems particles in every reported frame as numpy array of shape
[n_frames, n_particles, 3] with units of nanometers/picoseconds.
kinetic_energy: unit.Quantity
Kinetic energy of the system in every reported frame as numpy array of shape
[n_frames] with units of kilocalories/mole.
potential_energy: unit.Quantity
Potential energy of the system in every reported frame as numpy array of shape
[n_frames] with units of kilocalories/mole.
Examples
--------
>>> from uibcdf_test_systems import DoubleWell
>>> from uibcdf_test_systems.simulation import newtonian
>>> from simtk import unit
>>> double_well = DoubleWell(n_particles = 1, mass = 64 * unit.amu, Eo=4.0 * unit.kilocalories_per_mole, a=1.0 * unit.nanometers, b=0.0 * unit.kilocalories_per_mole))
>>> initial_coordinates = np.zeros([1, 3], np.float32) * unit.nanometers
>>> initial_velocities = np.zeros([1, 3], np.float32) * unit.nanometers/unit.picoseconds
>>> initial_coordinates[0,0] = 1.0 * unit.nanometers
>>> time, position, velocity, kinetic_energy, potential_energy = langevin_NVT(double_well,
>>> friction = 0.1/unit.picoseconds,
>>> initial_coordinates = initial_coordinates,
>>> initial_velocities = initial_velocities,
>>> integration_timestep = 0.02 * unit.picoseconds,
>>> saving_timestep = 0.5 * unit.picoseconds,
>>> total_time = 100 * unit.picoseconds)
Notes
-----
See the `corresponding documentation in the user guide regarding this method
<../../simulations/newtonian.html>`_.
Some simple examples on how this method is used can be found in the users guide sections
corresponding to `the free particle <../../systems/free_particle.html>`_, `the harmonic
well potential <../../systems/harmonic_well_potential.html>`_ or `the double well potential
<../../systems/double_well_potential.html>`_.
"""
from simtk.openmm import LangevinIntegrator, Platform, Context
from simtk import unit
import numpy as np
# System parameters.
n_particles = item.system.getNumParticles()
# Integrator.
integrator = LangevinIntegrator(temperature, friction, integration_timestep)
# Platform.
platform = Platform.getPlatformByName(platform_name)
# Simulation.
simulation = Simulation(item.topology, item.system, integrator, platform)
# Initial Context.
if initial_coordinates is None:
initial_coordinates = item.coordinates
simulation.context.setPositions(initial_coordinates)
if initial_velocities=='zeros' or initial_velocities is None:
initial_velocities = np.zeros([n_particles, 3], np.float32) * unit.nanometers/unit.picosecond
simulation.context.setVelocities(initial_velocities)
elif initial_velocities=='boltzmann':
simulation.context.setVelocitiesToTemperature(temperature)
else:
simulation.context.setVelocities(initial_velocities)
# Reporters.
default_reporter = False
tqdm_reporter = False
if reporters is None:
reporters = []
if saving_timestep is not None and len(reporters)==0:
saving_steps_interval = int(saving_timestep/integration_timestep)
default_reporter = MolSysMTTrajectoryDictReporter(saving_steps_interval, time=True, coordinates=True,
potentialEnergy=True, kineticEnergy=True, box=True)
reporters.append(default_reporter)
for reporter in reporters:
simulation.reporters.append(reporter)
# Initial report
initial_state = simulation.context.getState(getEnergy=True, getPositions=True, getVelocities=True)
for reporter in reporters:
reporter.report(simulation, initial_state)
n_steps = int(time/integration_timestep)
if tqdm:
tqdm_reporter = TQDMReporter(100, n_steps)
simulation.reporters.append(tqdm_reporter)
simulation.step(n_steps)
if tqdm_reporter:
tqdm_reporter.finalize()
if default_reporter:
return default_reporter.finalize()
else:
pass
def test_reporter(tmpdir, get_fn):
pdb = PDBFile(get_fn('native.pdb'))
forcefield = ForceField('amber99sbildn.xml', 'amber99_obc.xml')
# NO PERIODIC BOUNDARY CONDITIONS
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=CutoffNonPeriodic,
nonbondedCutoff=1.0 * nanometers,
constraints=HBonds,
rigidWater=True)
integrator = LangevinIntegrator(300 * kelvin, 1.0 / picoseconds,
2.0 * femtoseconds)
integrator.setConstraintTolerance(0.00001)
platform = Platform.getPlatformByName('Reference')
simulation = Simulation(pdb.topology, system, integrator, platform)
simulation.context.setPositions(pdb.positions)
simulation.context.setVelocitiesToTemperature(300 * kelvin)
tmpdir = str(tmpdir)
hdf5file = os.path.join(tmpdir, 'traj.h5')
ncfile = os.path.join(tmpdir, 'traj.nc')
dcdfile = os.path.join(tmpdir, 'traj.dcd')
reporter = HDF5Reporter(hdf5file,
2,
coordinates=True,
time=True,
cell=True,
potentialEnergy=True,
kineticEnergy=True,
temperature=True,
velocities=True)
reporter2 = NetCDFReporter(ncfile,
2,
coordinates=True,
time=True,
cell=True)
reporter3 = DCDReporter(dcdfile, 2)
simulation.reporters.append(reporter)
simulation.reporters.append(reporter2)
simulation.reporters.append(reporter3)
simulation.step(100)
reporter.close()
reporter2.close()
reporter3.close()
with HDF5TrajectoryFile(hdf5file) as f:
got = f.read()
eq(got.temperature.shape, (50, ))
eq(got.potentialEnergy.shape, (50, ))
eq(got.kineticEnergy.shape, (50, ))
eq(got.coordinates.shape, (50, 22, 3))
eq(got.velocities.shape, (50, 22, 3))
eq(got.cell_lengths, None)
eq(got.cell_angles, None)
eq(got.time, 0.002 * 2 * (1 + np.arange(50)))
assert f.topology == md.load(get_fn('native.pdb')).top
with NetCDFTrajectoryFile(ncfile) as f:
xyz, time, cell_lengths, cell_angles = f.read()
eq(cell_lengths, None)
eq(cell_angles, None)
eq(time, 0.002 * 2 * (1 + np.arange(50)))
hdf5_traj = md.load(hdf5file)
dcd_traj = md.load(dcdfile, top=get_fn('native.pdb'))
netcdf_traj = md.load(ncfile, top=get_fn('native.pdb'))
# we don't have to convert units here, because md.load already
# handles that
assert hdf5_traj.unitcell_vectors is None
eq(hdf5_traj.xyz, netcdf_traj.xyz)
eq(hdf5_traj.unitcell_vectors, netcdf_traj.unitcell_vectors)
eq(hdf5_traj.time, netcdf_traj.time)
eq(dcd_traj.xyz, hdf5_traj.xyz)
def test_reporter_subset(tmpdir, get_fn):
pdb = PDBFile(get_fn('native2.pdb'))
pdb.topology.setUnitCellDimensions([2, 2, 2])
forcefield = ForceField('amber99sbildn.xml', 'amber99_obc.xml')
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=CutoffPeriodic,
nonbondedCutoff=1 * nanometers,
constraints=HBonds,
rigidWater=True)
integrator = LangevinIntegrator(300 * kelvin, 1.0 / picoseconds,
2.0 * femtoseconds)
integrator.setConstraintTolerance(0.00001)
platform = Platform.getPlatformByName('Reference')
simulation = Simulation(pdb.topology, system, integrator, platform)
simulation.context.setPositions(pdb.positions)
simulation.context.setVelocitiesToTemperature(300 * kelvin)
tmpdir = str(tmpdir)
hdf5file = os.path.join(tmpdir, 'traj.h5')
ncfile = os.path.join(tmpdir, 'traj.nc')
dcdfile = os.path.join(tmpdir, 'traj.dcd')
xtcfile = os.path.join(tmpdir, 'traj.xtc')
atomSubset = [0, 1, 2, 4, 5]
reporter = HDF5Reporter(hdf5file,
2,
coordinates=True,
time=True,
cell=True,
potentialEnergy=True,
kineticEnergy=True,
temperature=True,
velocities=True,
atomSubset=atomSubset)
reporter2 = NetCDFReporter(ncfile,
2,
coordinates=True,
time=True,
cell=True,
atomSubset=atomSubset)
reporter3 = DCDReporter(dcdfile, 2, atomSubset=atomSubset)
reporter4 = XTCReporter(xtcfile, 2, atomSubset=atomSubset)
simulation.reporters.append(reporter)
simulation.reporters.append(reporter2)
simulation.reporters.append(reporter3)
simulation.reporters.append(reporter4)
simulation.step(100)
reporter.close()
reporter2.close()
reporter3.close()
reporter4.close()
t = md.load(get_fn('native.pdb'))
t.restrict_atoms(atomSubset)
with HDF5TrajectoryFile(hdf5file) as f:
got = f.read()
eq(got.temperature.shape, (50, ))
eq(got.potentialEnergy.shape, (50, ))
eq(got.kineticEnergy.shape, (50, ))
eq(got.coordinates.shape, (50, len(atomSubset), 3))
eq(got.velocities.shape, (50, len(atomSubset), 3))
eq(got.cell_lengths, 2 * np.ones((50, 3)))
eq(got.cell_angles, 90 * np.ones((50, 3)))
eq(got.time, 0.002 * 2 * (1 + np.arange(50)))
assert f.topology == md.load(get_fn('native.pdb'),
atom_indices=atomSubset).topology
with NetCDFTrajectoryFile(ncfile) as f:
xyz, time, cell_lengths, cell_angles = f.read()
eq(cell_lengths, 20 * np.ones((50, 3)))
eq(cell_angles, 90 * np.ones((50, 3)))
eq(time, 0.002 * 2 * (1 + np.arange(50)))
eq(xyz.shape, (50, len(atomSubset), 3))
hdf5_traj = md.load(hdf5file)
dcd_traj = md.load(dcdfile, top=hdf5_traj)
netcdf_traj = md.load(ncfile, top=hdf5_traj)
xtc_traj = md.load(xtcfile, top=hdf5_traj)
# we don't have to convert units here, because md.load already handles that
eq(hdf5_traj.xyz, netcdf_traj.xyz)
eq(hdf5_traj.unitcell_vectors, netcdf_traj.unitcell_vectors)
eq(hdf5_traj.time, netcdf_traj.time)
eq(xtc_traj.time, netcdf_traj.time)
eq(dcd_traj.xyz, hdf5_traj.xyz)
eq(xtc_traj.xyz, hdf5_traj.xyz)
eq(dcd_traj.unitcell_vectors, hdf5_traj.unitcell_vectors)
def main():
parser = argparse.ArgumentParser(description='Runs local minimization on \
the protein-ligand complex using OpenMM')
parser.add_argument('-l',
'--ligand',
action='store',
nargs=1,
dest='ligand',
help='The ligand .pdb file to generate \
parameters for')
parser.add_argument('-x',
'--xml_ligand',
action='store',
nargs=1,
dest='xml',
help='The xml file containing ligand \
parameters - use full path if not in directory where \
this script is being executed from')
parser.add_argument('-p',
'--protein',
action='store',
nargs=1,
dest='protein',
help='The protein complex .pdb file')
parser.add_argument('-i',
'--input_directory',
action='store',
nargs=1,
dest='input',
default=['./'],
help='Directory where \
input pdb files are stored')
parser.add_argument('-o',
'--output_directory',
action='store',
nargs=1,
dest='output',
default=['./'],
help='Directory where \
output log should be written')
args = vars(parser.parse_args())
#Load in ligand file and parameters
ligand_pdbfile = PDBFile(args['input'][0] + '/' + args['ligand'][0])
ligand_system = parmed.load_file(args['xml'][0])
ligand_structure = load_topology(ligand_pdbfile.topology,
ligand_system,
xyz=ligand_pdbfile.positions)
#Load in protein complex file and force field
receptor_pdbfile = PDBFile(args['input'][0] + '/' + args['protein'][0])
receptor_pdbfile_name = args['protein'][0].split('.pdb')[-2]
omm_forcefield = ForceField('amber14-all.xml')
receptor_system = omm_forcefield.createSystem(receptor_pdbfile.topology)
receptor_structure = load_topology(receptor_pdbfile.topology,
receptor_system,
xyz=receptor_pdbfile.positions)
#Generate ligand-protein complex
complex_structure = receptor_structure + ligand_structure
complex_system = (complex_structure.createSystem(nonbondedMethod=NoCutoff,
nonbondedCutoff=9.0 *
angstrom,
constraints=HBonds,
removeCMMotion=False))
#Set up simulation parameters
integrator = LangevinIntegrator(300 * kelvin, 1 / picosecond,
0.002 * picoseconds)
simulation = Simulation(complex_structure.topology, complex_system,
integrator)
simulation.context.setPositions(complex_structure.positions)
#Run local minimization
simulation.minimizeEnergy()
positions = simulation.context.getState(getPositions=True).getPositions()
#Save minimized complex structure
PDBFile.writeFile(
simulation.topology, positions,
open(args['output'][0] + '/' + receptor_pdbfile_name + '_min.pdb',
'w'))
from simtk.openmm import XmlSerializer, LangevinIntegrator, MonteCarloBarostat, Platform
# Initialization
with open("restrained.xml", "r") as f:
system = XmlSerializer.deserialize(f.read())
coords = PDBFile(os.path.join('simulations', 'npt_production', 'input.pdb'))
dt = 4.0 * unit.femtoseconds
Temp = 298.15 * unit.kelvin
Pres = 1.01325 * unit.bar
out_freq = 2500
print_freq = 50000
MD_steps = 12500000
bar_freq = int(MD_steps / print_freq)
integrator = LangevinIntegrator(Temp, 1.0 / unit.picoseconds, dt)
barostat = MonteCarloBarostat(Pres, Temp, 100)
system.addForce(barostat)
# Simulation Object
simulation = Simulation(coords.topology, system, integrator,
Platform.getPlatformByName('CUDA'), {
'CudaDeviceIndex': '0',
'CudaPrecision': 'single'
})
simulation.context.setPositions(coords.positions)
simulation.reporters.append(
DCDReporter(os.path.join('simulations', 'npt_production', 'test.dcd'),
out_freq, False))
simulation.reporters.append(
# Solvate
print('Adding solvent...')
# we use the 'padding' option to define the periodic box. The PDB file does not contain any
# unit cell information so we just create a box that has a 10A padding around the complex.
modeller.addSolvent(system_generator.forcefield,
model='tip3p',
padding=10.0 * unit.angstroms)
print('System has %d atoms' % modeller.topology.getNumAtoms())
with open(output_complex, 'w') as outfile:
PDBFile.writeFile(modeller.topology, modeller.positions, outfile)
# Create the system using the SystemGenerator
system = system_generator.create_system(modeller.topology,
molecules=ligand_mol)
integrator = LangevinIntegrator(temperature, 1 / unit.picosecond,
0.002 * unit.picoseconds)
system.addForce(
openmm.MonteCarloBarostat(1 * unit.atmospheres, temperature, 25))
print('Default Periodic box:', system.getDefaultPeriodicBoxVectors())
simulation = Simulation(modeller.topology,
system,
integrator,
platform=platform)
context = simulation.context
context.setPositions(modeller.positions)
print('Minimising ...')
simulation.minimizeEnergy()
# Write out the minimised PDB. The 'enforcePeriodicBox=False' bit is important otherwise the different
pdb.topology,
nonbondedMethod=app.NoCutoff,
nonbondedCutoff=500.0 * unit.angstroms,
switchDistance=496.0 * unit.angstroms,
)
system = apply_opls_combo(system, switching_distance=496.0 * unit.angstroms)
with open('QUBE_pro_out.xml', 'w') as outfile:
serialized_system = XmlSerializer.serialize(system)
outfile.write(serialized_system)
# Create the integrator to do Langevin dynamics
integrator = LangevinIntegrator(
298.15 * unit.kelvin, # Temperature of heat bath
1.0 / unit.picoseconds, # Friction coefficient
2.0 * unit.femtoseconds, # Time step
)
platform = Platform.getPlatformByName('CPU')
simulation = app.Simulation(pdb.topology, system, integrator, platform)
simulation.context.setPositions(pdb.positions)
print('energy from openmm library')
print(simulation.context.getState(getEnergy=True).getPotentialEnergy())
# platform.setPropertyValue(simulation.context, property='Precision', value='double')
# Minimize the energy
# print('Minimizing energy')
# Minimize(simulation, iters=0)
# atom_index_i atom_index_j r0 k
with open(opt.bond_restraints) as input_file:
for line in input_file:
columns = line.split()
atom_index_i = int(columns[0])
atom_index_j = int(columns[1])
r0 = float(columns[2])
k = float(columns[3])
flat_bottom_force.addBond(atom_index_i, atom_index_j, [r0, k])
print(
'Adding %sA distance restraints (k=%s kcal/mol/A^2) between %s and %s'
% (r0, k, atom_index_i, atom_index_j))
sys.stdout.flush()
system.addForce(flat_bottom_force)
integrator = LangevinIntegrator(opt.temp * unit.kelvin, 1 / unit.picosecond,
opt.timestep * unit.femtoseconds)
#system.addForce(openmm.MonteCarloBarostat(1*unit.atmospheres, opt.temp * unit.kelvin, 25))
print('Default Periodic box:', system.getDefaultPeriodicBoxVectors())
simulation = Simulation(modeller.topology,
system,
integrator,
platform=platform)
context = simulation.context
context.setPositions(modeller.positions)
# # Save to Gromacs format File
# # Save Protein-Ligand Complex
# structure = parmed.openmm.load_topology(modeller.topology, system, xyz=modeller.positions)
# structure.save('Cmp.pdb', overwrite=True)
# #structure.save('Cmp.gro', format='gro', overwrite=True)