Psi4 QM Geometry Optimization

Category Paths

  • 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

Optimize 3D geometry of the input molecules using Psi4. By default this Floe assumes you have one conformer per record. If you would like to geometry optimize all conformers, make sure to turn the Split Conformer for Optimizations switch to On. Split conformers will be remerged into their original primary molecule. The Geometry optimization can be performed with or without all torsions constrained.

Promoted Parameters

Title in user interface (promoted name)

Inputs

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

  • Required

  • Type: data_source

Outputs

Geometry Optimization Output (out): Dataset to store geometry optimized molecules.

  • Required

  • Type: dataset_out

  • Default: psi4_gopt

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

  • Required

  • Type: dataset_out

  • Default: psi4_gopt_failures

Geometry Optimization Options

Constrain Torsions (psi4_constrain_torsions): Chose to constrain torsions around all rotatable bonds (On), otherwise (Off) all degrees of freedom will be optimized.

  • Required

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Constrain Torsions with Polar Hydrogens (constrain_polar_hydrogens): This parameter only applies if the ‘Constrain torsion’ parameter is also On. Torsions terminating in a polar hydrogen (i.e. hydroxyl groups) will be constrained along with all other rotatable bonds (On). Otherwise (Off), only rotatable bonds with heavy atoms will be constrained.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Split Conformer for Optimization (split_switch): For multi-conformer molecules, switch on to optimize each conformer separately. If Off, for a multi-conformer molecule only the first conformer will be optimized.

  • Required

  • Type: boolean

  • Default: False

  • Choices: [True, False]

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’, ‘PBE’, ‘PBE0’]

Psi4 Basis Set (Geometry Optimization) (psi4_gopt_basis): Basis set for Psi4 geometry optimization.

  • 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

Psi4 Advanced Parameter Options

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

Remove Implicit Hydrogens (remove_implicit_hydrogens): If True, implicit hydrogens are removed from the molecule before the formal charge is calculated. If false, the Cube will fail if the molecule does have implicit hydrogens.

  • Type: boolean

  • Default: False

  • Choices: [True, False]