Psi4 QM Local Minima Search

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

• Solution-based/Small Molecule Lead-opt/QM Analysis/Internal Energies

• Task-based/Quantum Mechanics/Energetic Analysis

• Role-based/Computational Chemist

• Product-based/Quantum Mechanics/Psi4

Description

This floe searches all the low energy minima of a input structure. A large ensemble of potential conformations are generated using OpenEye toolkits. These conformers are then optimized using Psi4. QM minima are deduplicated and filtered based on energy using a energy window.

This floe assumes that all input molecules are a part of the same ensemble. Since conformers are generated at the beginning, there is no reason to provide more than one input molecule. However, this floe will also work with multiple tautomers of the same molecule, if they are provided as input. The energy window is applied across all input molecules.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Input Dataset (in): The dataset(s) to read records from

• Required

• Type: data_source

Outputs

Intermediate Optimization Output (confgen_data_out): Dataset to store QM optimized conformers before deduplication. If a job is cancelled early (either by the user or because a cost threshold is reached), these intermediate optimized conformers will still be saved.

• Required

• Type: dataset_out

• Default: psi4_all_conf_gopt

Psi4 Local Minima Output (local_minima_out): Dataset to store optimized conformers in the specified energy window. Each record has a single conformer.

• Required

• Type: dataset_out

• Default: psi4_local_minima

Failure Output (failure): Dataset to store records which fail during this floe.

• Required

• Type: dataset_out

• Default: psi4_loc_min_failures

Conformer Floe Report Name (conf_report_name): Floe report title that summarizes conformer ensemble results.

• Type: string

• Default: Psi4 Conformer Report

Conformer Parameters

RMSD Threshold for conformer generation (confgen_rmsd_threshold): RMSD threshold for conformer duplicate removal

• Type: decimal

• Default: 0.5

Maximum Conformers for Geometry Optimization (limit_confs): This parameter limits the number of conformers optimized to prevent accidentally spending more than expected on a single floe. If more than this number of conformers are generated, then only one conformer will be optimized to learn about the cost of this floe/conformer. If the maximum number of conformers is set to 0, then ALL generated conformers are optimized.

• Type: integer

• Default: 100

Psi4 Energy Filter Window (kcal/mol) (psi4_e_window): Energy window of allowed strain. When the filter is set to -1 all records are output

• Type: decimal

• Default: 10.0

Psi4 Calculation Parameters

Psi4 Hamiltonian (Geometry Optimization) (psi4_gopt_method): Method used for Psi4 geometry optimization.

• Type: string

• Default: HF3c

• Choices: [‘HF3c’, ‘PBEh3c’, ‘HF’, ‘HF-D3’, ‘B3LYP’, ‘B3LYP-D3BJ’, ‘B3LYP-D3MBJ’, ‘B2PLYP-D3BJ’, ‘M06’, ‘M06-2X’, ‘M06-L’, ‘MN15-D3BJ’, ‘MN15-L’, ‘PW6B95-D3BJ’, ‘CAM-B3LYP’, ‘CAM-B3LYP-D3BJ’, ‘WB97X’, ‘WB97X-D’, ‘WB97M-D3BJ’, ‘B97M-D3BJ’, ‘PBE’, ‘PBE0’]

Psi4 Basis Set (Geometry Optimization) (psi4_gopt_basis): Basis set for Psi4 geometry optimization. Default empty basis set (‘’) goes with HF3c, which has one built in.

• Type: string

• Default:

• Choices: [‘’, ‘minix’, ‘6-31G’, ‘6-31G*’, ‘6-31+G*’, ‘6-31G**’, ‘6-31+G**’, ‘6-311G**’, ‘6-311+G**’, ‘6-311G(2d,2p)’, ‘def2-SVP’, ‘def2-SVPD’, ‘def2-TZVP’, ‘def2-TZVPD’, ‘def2-TZVPP’, ‘def2-TZVPPD’, ‘cc-pVDZ’, ‘aug-cc-pVDZ’, ‘cc-pVTZ’, ‘aug-cc-pVTZ’, ‘LanL2DZ’]

Psi4 Memory (psi4_gopt_memory): Memory for Psi4 calculations in MBs.

• Type: decimal

• Default: 14400

Psi4 #Threads (psi4_gopt_nthreads): Number of CPUs for Psi4 calculations.

• Type: integer

• Default: 8

Optimization Engine (psi4_engine): Choose an optimization engine from OptKing or GeomeTRIC.

• Type: string

• Default: Psi4 OptKing

• Choices: [‘Psi4 OptKing’, ‘Psi4 GeomeTRIC’]

Advanced Parameters

Psi4 Energy Field (psi4_energy_field): Field containing Psi4 energy.

• Type: field_parameter::float

• Default: Psi4 Energy (kcal/mol)

Psi4 Strain Energy Field (psi4_strain_energy_field): Field to store calculated strain energy.

• Required

• Type: field_parameter::float

• Default: Psi4 Strain Energy (kcal/mol)

Save Psi4 Log File (store_log_file): The log file generated from Psi4 is saved. It will be available as a floe report when the floe is complete.

• Type: boolean

• Default: False

• Choices: [True, False]

Report Name for Log Files (qm_log_report_name): Floe report to store QM log files. This report is only created if the calculation log files were stored.

• Type: string

• Default: Psi4 Log File Report