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’, ‘DZVP’, ‘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
Choices: [‘mmff94s’, ‘parsley’, ‘sage’]
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)