Multi-level approach to conformer ensemble of crystal polymorphs (Parts I+II of CSP Protocol)¶
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
failure (dataset_out) : Dataset containing records with failed jobs from three stages of computation: qm multipoles, IEFF, or crystal visualization.Default: failure unique_confs (dataset_out) : Resulting dataset with all unique conformers in top IEFF crystal structures after rigid packing.Default: unique_confs in (data_source) : Dataset with input molecules on which crystal polymorph predictions need to be performed. out (dataset_out) : Resulting dataset with lowest in energy, deduplicated crystal structures (in the CIF format) predicted with IEFF Crystal Force Field.Default: top_structures omega_confs (dataset_out) : Resulting dataset with all omega conformations.Default: omega_confs qm_confs (dataset_out) : Resulting dataset with qm ensemble of conformations.Default: qm_ensemble in_ref (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.
Extra Required Parameters
Switch (boolean) : This parameter controls whether records are sent to the ‘true’ or ‘false’ portDefault: True Switch (boolean) : This parameter controls whether records are sent to the ‘true’ or ‘false’ portDefault: True Switch (boolean) : This parameter controls whether records are sent to the ‘true’ or ‘false’ portDefault: True Output Shard Format (string) : The format of the data that shards will containDefault: oedbChoices: oedb, ism.gz, oez, oeb.gz, oeb records_per_shard (integer) : The target number of records in a shard. 0 indicates to run up to the max_shard_bytes limit per shardDefault: 10 QM Multipoles Switch (boolean) : Controls if QM Multipoles are computed or this step is skipped.Default: True Random Packing Switch (boolean) : Controls if Random Packing of monomer in crystal is performed or skipped.Default: True Hit List Size (integer) : The desired size of the hit list.Default: 1 Min: 1 Psi4 Energy Field (Field Type: Float) : Psi4 Energy fieldDefault: Psi4 Energy (kcal/mol) Temp Collection Name (collection_sink) : Name for the created collections.Default: IEFF Temp Crystal Packings Collection Hit List Size (integer) : The desired size of the hit list.Default: 1 Min: 1 Energy tag for global minimum (Field Type: Float) : Energy tag for lattice energy in order to find the global minimum.Default: IEFF Lattice Full Energy (kcal/mol) Collection Name (collection_sink) : Name for the created collections.Default: IEFF Crystal Packings Collection Output Shard Format (string) : The format of the data that shards will containDefault: oedbChoices: oedb, ism.gz, oez, oeb.gz, oeb Records per shard parameter (integer) : Number of records in each shard. For optimal performance the combination of parameters: ‘Size of the batch’ (batch_size), ‘Parallel Group Item Count’ (item_count), and ‘Records per shard parameter’ (records_per_shard) need to satisfy : records_per_shard = batch_size * item_countDefault: 50