espaloma.data.md.MoleculeVacuumSimulation

class espaloma.data.md.MoleculeVacuumSimulation(forcefield='gaff-1.81', n_samples=100, n_conformers=10, n_steps_per_sample=1000, temperature=Quantity(value=350, unit=kelvin), collision_rate=Quantity(value=1.0, unit=/picosecond), step_size=Quantity(value=1.0, unit=femtosecond), charge_method=None)[source]

Bases: object

Simluate a single molecule system in vaccum.

Parameters

  • g (espaloma.Graph) – Input molecular graph.

  • n_samples (int) – Number of samples to collect.

  • n_steps_per_sample (int) – Number of steps between each sample.

  • temperature (float * unit.kelvin) – Temperature for the simluation.

  • collision_rate (float / unit.picosecond) – Collision rate.

  • timestep (float * unit.femtosecond) – Time step.

simulation_from_graph : Create simluation from molecule.
run : Run the simluation.
__init__(forcefield='gaff-1.81', n_samples=100, n_conformers=10, n_steps_per_sample=1000, temperature=Quantity(value=350, unit=kelvin), collision_rate=Quantity(value=1.0, unit=/picosecond), step_size=Quantity(value=1.0, unit=femtosecond), charge_method=None)[source]

Methods

__init__([forcefield, n_samples, ...])

run(g[, in_place])

Collect samples from simulation.

simulation_from_graph(g)

Create simulation from moleucle
run(g, in_place=True)[source]

Collect samples from simulation.

Parameters

  • g (esp.Graph) – Input graph.

  • in_place (bool) – If ture,

Returns

  • samples (torch.Tensor, shape=(n_samples, n_nodes, 3)) – in_place=True Sample.

  • graph (esp.Graph) – Modified graph.

simulation_from_graph(g)[source]

Create simulation from moleucle