Python Yank.mc_displacement_sigma Exemples

Exemple #1

Fichier : mhc-peptide-tcr.py Projet : dprovasi/yank

    # Identify various components.
    solvated_topology_mdtraj = mdtraj.Topology.from_openmm(solvated_topology_openmm)
    atom_indices[phase] = dict()
    for component in components:
        atom_indices[phase][component] = solvated_topology_mdtraj.select(component_dsl[component])

    # DEBUG
    print "Atom indices of ligand:"
    print atom_indices[phase]['ligand']

# Create list of phase names.
phases = systems.keys()

# Create reference thermodynamic state.
from yank.repex import ThermodynamicState # TODO: Fix this weird import path to something more sane, like 'from yank.repex import ThermodynamicState'
if is_periodic:
    thermodynamic_state = ThermodynamicState(temperature=temperature, pressure=pressure)
else:
    thermodynamic_state = ThermodynamicState(temperature=temperature)

# TODO: Select protocols.

# Turn off MC ligand displacement.
yank.mc_displacement_sigma = None

# Create new simulation.
yank.create(phases, systems, positions, atom_indices, thermodynamic_state, options=options)

# TODO: Write PDB files

Exemple #2

    # DEBUG
    print "Atom indices of ligand:"
    print atom_indices[phase]['ligand']

# Create list of phase names.
phases = systems.keys()

# Create reference thermodynamic state.
from yank.repex import ThermodynamicState  # TODO: Fix this weird import path to something more sane, like 'from yank.repex import ThermodynamicState'
if is_periodic:
    thermodynamic_state = ThermodynamicState(temperature=temperature,
                                             pressure=pressure)
else:
    thermodynamic_state = ThermodynamicState(temperature=temperature)

# TODO: Select protocols.

# Turn off MC ligand displacement.
yank.mc_displacement_sigma = None

# Create new simulation.
yank.create(phases,
            systems,
            positions,
            atom_indices,
            thermodynamic_state,
            options=options)

# TODO: Write PDB files