Psi4 QM Complete Molecule Torsion Scan

Category Paths

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

  • Solution-based/Small Molecule Lead-opt/QM Analysis/Torsions & Strain

  • Role-based/Computational Chemist

  • Task-based/Quantum Mechanics/Torsion Sampling

  • Product-based/Quantum Mechanics/Psi4

Description

This floe performs a 1D torsion scan on all rotatable bonds in the input molecule.

Scanning is performed with the OETorsionScan function from OESzybki TK at a specified resolution (in degrees). This function includes a force field minimization of all internal degrees of freedom except for the selected torsion.

An optional QM calculation is performed with Psi4, either an optimization (Optimization Switch=True) or a single point energy (SPE) calculation (Optimization Switch=False). In the case of the QM optimization, the torsion is constrained and all other degrees of freedom are relaxed further.

The output of this floe is a multiconformer molecule for each input molecule, where each conformer represents one angle from the torsion scan.

The entire molecule is included for each calculation on each torsion angle. For larger molecules and those with many rotatable bonds, this can get expensive. Consider running Psi4 QM Fragmentation and Torsion Scanning instead. In that floe, a torsion scan is run for each rotatable bond, but the molecule is fragmented to allow for more cost-efficient calculations.

Promoted Parameters

Title in user interface (promoted name)

Inputs

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

  • Required

  • Type: data_source

Outputs

Psi4 Torsion Scan Output (out): Dataset to store torsion scan output records.

  • Required

  • Type: dataset_out

  • Default: psi4_complete_torscan

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

  • Required

  • Type: dataset_out

  • Default: psi4_torscan_failures

Floe Report Name (tors_report_name): Title for the torsion scan floe report.

  • Type: string

  • Default: Psi4 Torsion Scan Report

Torsion Scan Parameters

Torsion Increment (resolution): Torsion angle increment in degrees

  • Type: decimal

  • Default: 5.0

QM Switch (QM_switch): When turned On, a QM calculation is performed; either single point energy or optimization is set with the Optimization Switch parameter. When turned Off, only the force field energies are reported for each torsion scan.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Optimization Switch (adiabatic_switch): When turned On, a geometry optimization is performed constraining only the scanned torsion. When turned Off, a single point energy calculation is performed on the force field optimized conformers.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Psi4 Calculation Parameters

Psi4 Hamiltonian (psi4_method): Hamiltonian used for geometry optimization or single point energy calculation.

  • 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 (psi4_basis): Basis set used for geometry optimization or single point energy calculation.

  • 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_memory): Memory for Psi4 calculations in MBs.

  • Type: decimal

  • Default: 14400

Psi4 #Threads (psi4_nthreads): Number of CPUs for Psi4 calculations.

  • Type: integer

  • Default: 8

QM Engine (psi4_engine): Chose an engine for the geometry optimization. Psi4

supports both OptKing and GeomeTRIC.

  • Type: string

  • Default: Psi4 GeomeTRIC

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

Advanced Parameters

Save Psi4 Log Files (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 Force Field Parameters

Force Field (ff_type): Built-in force field model to be used.

  • Type: string

  • Default: sage_openff200

  • Choices: [‘mmff94s’, ‘smirnoff99frost’, ‘parsley_openff100’, ‘parsley_openff111’, ‘parsley_openff121’, ‘parsley_openff131’, ‘sage_openff200’]

Penalty Force Constant (force_constant): Force constant used to apply the dihedral constraint.

  • Type: decimal

  • Default: 100000

None (solvent_model): Solvent model to be used

  • Type: string

  • Default: Gas-phase

  • Choices: [‘Gas-phase’, ‘Sheffield’, ‘SheffieldPB’]

Force Field Energy Field (ff_en_field): Name of field for storing force field energies.

  • Type: field_parameter::float

  • Default: FF Energy (kcal/mol)