complex_coordinates = units.Quantity(numpy.zeros([2, 3], numpy.float64),
units.angstroms)
complex_coordinates[1, 0] = 10.0 * units.angstroms
# Create temporary directory for testing.
import tempfile
output_directory = tempfile.mkdtemp()
# Initialize YANK object.
from yank import Yank
yank = Yank(receptor=receptor_system,
ligand=ligand_system,
complex_coordinates=[complex_coordinates],
output_directory=output_directory)
yank.solvent_protocol = yank.vacuum_protocol
yank.complex_protocol = yank.vacuum_protocol
yank.restraint_type = 'flat-bottom'
yank.temperature = temperature
yank.niterations = 100
yank.platform = openmm.Platform.getPlatformByName("Reference")
# Run the simulation.
yank.run()
#
# Analyze the data.
#
results = yank.analyze()
# TODO: Check results against analytical results.
#receptor_system.addForce(force)
# Create complex coordinates.
import simtk.unit as units
complex_coordinates = units.Quantity(numpy.zeros([2,3], numpy.float64), units.angstroms)
complex_coordinates[1,0] = 10.0 * units.angstroms
# Create temporary directory for testing.
import tempfile
output_directory = tempfile.mkdtemp()
# Initialize YANK object.
from yank import Yank
yank = Yank(receptor=receptor_system, ligand=ligand_system, complex_coordinates=[complex_coordinates], output_directory=output_directory)
yank.solvent_protocol = yank.vacuum_protocol
yank.complex_protocol = yank.vacuum_protocol
yank.restraint_type = 'flat-bottom'
yank.temperature = temperature
yank.niterations = 100
yank.platform = openmm.Platform.getPlatformByName("Reference")
# Run the simulation.
yank.run()
#
# Analyze the data.
#
results = yank.analyze()
# TODO: Check results against analytical results.
