propertyestimator.protocols.utils.generate_gradient_protocol_group

propertyestimator.protocols.utils.generate_gradient_protocol_group(template_reweighting_protocol, force_field_path, coordinate_file_path, trajectory_file_path, statistics_file_path, replicator_id='repl', substance_source=None, id_suffix='', enable_pbc=True, effective_sample_indices=None)[source]

Constructs a set of protocols which, when combined in a workflow schema, may be executed to reweight a set of existing data to estimate a particular property. The reweighted observable of interest will be calculated by following the passed in analysis_protocol.

Parameters

  • template_reweighting_protocol (BaseMBARProtocol) –

    A template protocol which will be used to reweight the observable of interest to small perturbations to the parameter of interest. These will then be used to calculate the finite difference gradient.

    The template must have it’s reference_reduced_potentials input set. The target_reduced_potentials input will be set automatically by this function.

    In the case that the template is of type ReweightStatistics and the observable is an energy, the statistics path will automatically be pointed to the energies evaluated using the perturbed parameter as opposed to the energy measured during the reference simulation.

  • force_field_path (ProtocolPath) –

    The path to the force field parameters which the observables are being

    estimated at.

  • coordinate_file_path (ProtocolPath) – A path to the initial coordinates of the simulation trajectory which was used to estimate the observable of interest.

  • trajectory_file_path (ProtocolPath) – A path to the simulation trajectory which was used to estimate the observable of interest.

  • statistics_file_path (ProtocolPath, optional) – A path to the statistics which were generated alongside the trajectory passed to the trajectory_file_path. These should have been generated using the passed force_field_path.

  • replicator_id (str) – A unique id which will be used for the protocol replicator which will replicate this group for every parameter of interest.

  • substance_source (PlaceholderInput, optional) – An optional protocol path to the substance whose gradient is being estimated. If None, the global property substance is used.

  • id_suffix (str) – An optional string to append to the end of each of the protocol ids.

  • enable_pbc (bool) – If true, periodic boundary conditions are employed when recalculating the reduced potentials.

  • effective_sample_indices (ProtocolPath, optional) – A placeholder variable which in future will ensure that only samples with a non-zero weight are included in the gradient calculation.

Returns

  • ProtocolGroup – The protocol group which will estimate the gradient of an observable with respect to one parameter.

  • ProtocolReplicator – The replicator which will copy the gradient group for every parameter of interest.

  • ProtocolPath – A protocol path which points to the final gradient value.