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()
#force.addParticle(0, []) #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()