Multi-level approach to conformer ensemble of crystal polymorphs (Parts I+II of CSP Protocol)

Category Paths

  • Solution-based/Formulation

  • Role-based/Formulation Scientist

  • Product-based/Crystal Structure Prediction

  • Task-based/Crystal Structure Prediction

Description

This Floe implements multi-level sampling of conformational ensemble of crystal polymorphs. At each level, generated conformers are packed with intermolecular force field. At subsequent levels, the conformer sampling resolution is finer, but only those conformers are kept, that are similar to conformers of low energy polymorphs from previous level. The following four levels could be used, with Omega RMSD threshold parameter equal to: 1.0A, 0.75A, 0.5A, and 0.25A. To implement such protocol, this Floe needs to be run four times, with respective adjustment of the threshold parameter. Starting from second level, reference conformers from previous level need to be input to the Floe.

Promoted Parameters

Title in user interface (promoted name)

  • Dataset with Failed Calculations (failure) type: dataset_out: Dataset containing records with failed jobs from three stages of computation: qm multipoles, IEFF, or crystal visualization.
    Default: failure
  • Input Molecules (in) type: data_source: Dataset with input molecules on which crystal polymorph predictions need to be performed.
  • Input Reference Conformers (in_ref) type: data_source: Optional dataset with reference conformers. When no input is provided, all generated conformers are kept, otherwise, only those similar to reference conformers are kept in the workflow.
  • Dataset with omega conformations (omega_confs) type: dataset_out: Resulting dataset with all omega conformations.
    Default: omega_confs
  • Predicted Crystal Structures (out) type: dataset_out: Resulting dataset with lowest in energy, deduplicated crystal structures (in the CIF format) predicted with IEFF Crystal Force Field.
    Default: top_structures
  • Dataset with qm conformational geometries (qm_confs) type: dataset_out: Resulting dataset with qm ensemble of conformations.
    Default: qm_ensemble
  • Dataset with unique conformers in top packings (unique_confs) type: dataset_out: Resulting dataset with all unique conformers in top IEFF crystal structures after rigid packing.
    Default: unique_confs

Parameter title in user interface (promoted name)

  • QM Multipoles Switch (switch) type: boolean: Controls if QM Multipoles are computed or this step is skipped.
    Default: True

Parameter title in user interface (promoted name)

  • Random Packing Switch (switch) type: boolean: Controls if Random Packing of monomer in crystal is performed or skipped.
    Default: True

Parameter title in user interface (promoted name)

  • Temp Collection Name (collection_name) type: collection_sink: Name for the created collections.
    Default: IEFF Temp Crystal Packings Collection

Parameter title in user interface (promoted name)

  • Collection Name (collection_name) type: collection_sink: Name for the created collections.
    Default: IEFF Crystal Packings Collection