cgexplore.optimisation.CGOMMDynamics

class cgexplore.optimisation.CGOMMDynamics(fileprefix, output_dir, temperature, num_steps, time_step, friction, reporting_freq, traj_freq, random_seed=None, max_iterations=None, atom_constraints=None, platform=None)[source]

Bases: CGOMMOptimizer

Optimiser of CG models using OpenMM and Molecular Dynamics.

Methods

run_dynamics

Run dynamics on an assigned system.
Parameters:

  • fileprefix (str)

  • output_dir (Path)

  • temperature (Quantity)

  • num_steps (int)

  • time_step (Quantity)

  • friction (Quantity)

  • reporting_freq (float)

  • traj_freq (float)

  • random_seed (int | None)

  • max_iterations (int | None)

  • atom_constraints (Iterable[tuple[int, int]] | None)

  • platform (str | None)

calculate_energy(assigned_system)

Calculate energy of a system.

Parameters:

assigned_system (AssignedSystem | MartiniSystem)

Return type:

float

calculate_energy_decomposition(assigned_system)

Calculate energy of a system.

Parameters:

assigned_system (AssignedSystem | MartiniSystem)

Return type:

dict[str, float]

optimize(assigned_system)

Optimize a molecule.

Parameters:

assigned_system (AssignedSystem | MartiniSystem)

Return type:

Molecule

read_final_energy_decomposition()

Read the final energy decomposition in an output file.

Return type:

dict[str, tuple[float, str]]

run_dynamics(assigned_system)[source]

Run dynamics on an assigned system.

Parameters:

assigned_system (AssignedSystem | MartiniSystem)

Return type:

OMMTrajectory