Gaussian QM Geometry Optimization¶
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Solution-based/Small Molecule Lead-opt/QM Analysis
Task-based/Quantum Mechanics/Energetic Analysis
Role-based/Computational Chemist
Product-based/Quantum Mechanics/Gaussian
Description
This floe optimizes the 3D geometry of the input molecules (or conformers) using Gaussian. Choose a level of theory for the calculation and the settings for implicit solvent.
This calculation will not generate 3D conformers for the input molecule; it only optimizes the existing geometries.
By default this floe assumes you have one conformer per record. If you would like to optimize all conformers of a multiconformer molecule, make sure to turn the Split Conformers switch to On. Optimized geometries for split conformers will be merged back into their original primary molecule and the results will be found on the conformer record; it must be expanded to view in Spreadsheets.
The default Hardware Requirements should be sufficient for most drug-like molecules at the default level of theory; consider changing these settings when running calculations with a larger basis set. The Gaussian Geometry Optimizer Cube has metrics enabled which can be monitored during a calculation to verify the settings are sufficient.
At this time, only a full geometry optimization can be performed. Options for constraints in the optimization will be available in the future. If you need to perform a constrained optimization at this time, see the Gaussian QM Run Input Files Floe to run any calculation with a Gaussian input file.
Promoted Parameters
Title in user interface (promoted name)
Inputs
Input Dataset (in): The dataset(s) to read records from
Required
Type: data_source
Outputs
Gaussian Output (out): Output dataset to write to
Required
Type: dataset_out
Default: Gaussian_Gopt
Failure Output (failure): Output dataset to write to
Required
Type: dataset_out
Default: Gaussian_Gopt_Failures
Save Log files (store_log_file): Save output log files for all calculations, they are always saved for failed calculations.
Type: boolean
Default: False
Choices: [True, False]
Report Name for Log Files (gau_log_report_name): Gaussian log files for the calculation are saved to a floe report. Log files are saved for all failures and optionally saved for successful calculations if the Store Log Files above is turned On.
Type: string
Default: Gaussian Log File Report
Gaussian Calculation Parameters
Split Conformer (split_switch): For multiconformer molecules, switch On to optimize each conformer separately.
Required
Type: boolean
Default: False
Choices: [True, False]
Gaussian Solvent Environment (solvent): Solvent environment used for this Gaussian calculation
Type: string
Default: Gas Phase
Choices: [‘Gas Phase’, ‘Water IEFPCM’, ‘Water CPCM’, ‘Water SMD’, ‘DMSO IEFPCM’, ‘DMSO CPCM’, ‘DMSO SMD’, ‘Octanol IEFPCM’, ‘Octanol CPCM’, ‘Octanol SMD’]
Gaussian Method (method): Method used for this Gaussian calculation
Type: string
Default: HF
Choices: [‘HF’, ‘B3LYP’, ‘B3LYP - GD3’, ‘B3LYP - GD3BJ’, ‘B2PLYP’, ‘B2PLYPD3’, ‘M06’, ‘M062X’, ‘M06L’, ‘MN15’, ‘MN15L’, ‘PW6B95D3’, ‘CAM-B3LYP’, ‘CAM-B3LYP - GD3’, ‘CAM-B3LYP - GD3BJ’, ‘WB97X’, ‘wB97XD’, ‘LC-wHPBE’, ‘PBE1PBE’, ‘MP2’, ‘PW91PW91’, ‘PM6’]
Gaussian Basis Set (basis): Basis set used for property calculation with Gaussian
Type: string
Default: 6-31G
Choices: [‘3-21G’, ‘6-31G’, ‘6-31G*’, ‘6-31+G*’, ‘6-31G**’, ‘6-31+G**’, ‘6-311G**’, ‘6-311+G**’, ‘6-311G(2d,2p)’, ‘def2SVP’, ‘def2TZVP’, ‘def2TZVPP’, ‘aug-cc-pvdz’, ‘aug-cc-pvtz’, ‘’]
Hardware Requirements for Gaussian Calculation
Gaussian # Threads (gaussian_nthreads): Number of CPUs for Gaussian calculation.
Type: integer
Default: 8
Gaussian Memory (gaussian_memory): Memory for Gaussian calculations in MBs.
Type: decimal
Default: 14400
Gaussian Disk Space (gaussian_disk_space): Temporary disk space (in MB) required for your calculation.
Type: decimal
Default: 25600
Advanced
Gaussian Energy Field (energy_field): Field created during Floes to store Gaussian Energy
Type: field_parameter::float
Default: Gaussian Energy (kcal/mol)
Remove Implicit Hydrogens (remove_implicit_hydrogens): If True, implicit hydrogens are removed from the molecule before the formal charge is calculated. This is recommended when a molecule was created from an XYZ file or similar, since bond orders based on coordinates can lead to extra implicit hydrogens If false, the Cube will fail if the molecule does have implicit hydrogens.
Type: boolean
Default: False
Choices: [True, False]
Timeout for Gaussian Calculation (Hours) (gau_timeout): Parallel Cubes have a strict time limit, this parameter stops the gaussian calculation before it reaches that limit. Note, this is a maximum only, the cube will finish when the calculation finishes if it is less than the time limit.
Type: decimal
Default: 10
Maximum number of retries (gau_retries): Maximum number of attempts to perform QM calculation
Type: integer
Default: 3