Water Sampling FloeΒΆ

Category Paths

  • Solution-based/Formulation

  • Role-based/Formulation Scientist

  • Product-based/Crystal Structure Prediction

  • Task-based/Crystal Structure Prediction

Description

This Floe samples waters around each input conformer and assess the relative energy of the resulting dimers. It assumes all input conformers are of the same molecule.

Promoted Parameters

Title in user interface (promoted name)

  • Energy thresholds (energy_thresholds) type: string: Energy thresholds for water re-sampling stage.
    Default: 0.0,2.5,5.0
  • Failed Conformation (failure) type: dataset_out: Dataset containing records with (failed) water sampling.
    Default: monohydrate_failures
  • Force Field (force_field) type: string: Force Field used in water sampling.
    Default: ieff3
    Choices: ieff2, ieff3, smirnoff
  • Hydrogen-Hydrogen deduplication Tolerance (hydrogen_hydrogen_dedup_tol) type: decimal: Hydrogen-Hydrogen deduplication Tolerance.
    Default: 0.5
  • Input monomer geometries (in) type: data_source: Dataset containing input monomer geometries for which we want to sample waters.
  • Input reference geometry (in_ref) type: data_source: Dataset containing input reference geometry.
  • Number of waters per site (num_waters_per_site) type: integer: Number of most diverse waters per donor/acceptor site. When zero, all waters in energy window will be kept.
    Default: 10
  • Number of waters for re-sampling (num_waters_resampling) type: string: Number of waters per relative energy range for water re-sampling stage.
    Default: 20,10,5
  • Output Dataset with results of Water Sampling (out) type: dataset_out: Resulting dataset containing records with Phonon Frequency Spectrum, Crystal Entropy.
    Default: monohydrate
  • Oxygen-Oxygen deduplication Tolerance (oxygen_oxygen_dedup_tol) type: decimal: Oxygen-Oxygen deduplication Tolerance.
    Default: 0.26
  • Dataset with computed QM multipoles (qm_mults) type: dataset_out: Resulting dataset with computed QM Multipoles.
    Default: qm_mults
  • Multipoles Switch (qm_mults_switch) type: boolean: Boolean switch that controls whether multipoles need to be done on the conformers.
    Default: True
  • Water RMSD Switch (water_rmsd_switch) type: boolean: When On, compares and filters sampled waters to a reference (experimental) monohydrate.
    Default: False
  • Water RMSD filtering threshold (water_rmsd_threshold) type: decimal: Water RMSD distances between simulated and reference monohydrates above threshold will be filtered away.
    Default: 2.0
  • Memory in MB of the Water Sampling Cube (water_sampling_memory) type: decimal: Memory given to the water sampling cube.
    Default: 14400 , Min: 256.0, Max: 8589934592