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 (omega_max_confs): Set the maximum conformers to be generated with Omega. Note the more conformers the more expensive the QM optimizations will be.
Type: integer
Default: 100
Omega Energy Window (conf_en_window): Energy window used for conformer generation in Omega
Type: decimal
Default: 50.0
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’, ‘DZVP’, ‘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
Advanced Conformer Generation Options
Switch (csp_conf_switch): Use the extra dense conformer generation developed for OpenEye’s
crystal structure prediction protocol. In this algorithm, all fragment enumeration is maintained during deduplication.
Required
Type: boolean
Default: False
Choices: [True, False]
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