Gaussian QM Torsion Scan Tutorial¶
Running this Floe with provided input molecule and parameters specified in this tutorial will cost around $1.20. Navigate through the categories Product-based / Quantum Mechanics / Gaussian to find this Floe. Then, locate or search for “Gaussian QM UI Torsion Scan.”
In this Floe, a torsion is selected with the Orion Sketcher. A force field torsion scan is generated with the Szybki Toolkit. Then, a QM single point energy or geometry optimization is performed with the specified torsion constrained. A Floe Report is generated to illustrate the scanned torsions. If a reference molecule is provided then the torsion in that molecule is indicated in the report.
There are two other torsion scanning Floes where the torsions are specified with different mechanisms. SMARTS patterns are used in the Gaussian QM SMARTS Torsion Scan Floe and every rotatable bond is scanned in the Gaussian QM Fragmentation and Torsion Scan Floe.
The input for this tutorial (Hydroxymethyl-benzoic-acid) can be found in the “QM Gaussian Floes” folder of the Tutorial Data on Orion. This will be used for the both input datasets in the Floe: Select Torsion Input and Reference Dataset (Optional).
For the tutorial, set the Torsion Increment to 15 and change the Gaussian Solvent Environment parameter to “Water PCPM” As shown in the input form below:
After clicking on the “Choose Input…” button next to Select Torsion Input an Orion sketcher will appear. The molecule can be sketched or an input dataset can be selected. After loading the provided molecule, the torsion around the methanol group is selected. The lasso tool can be used to select any 4 contiguous atoms.
Make sure the Hydroxymethyl-benzoic-acid dataset is also set for the Reference Dataset (Optional) dataset. Select the start button at the bottom of the form to submit the job.
Navigate to the jobs tab and select the running Floe. While the job is running the cubes will be colored by which are complete, in progress, or pending. In all Gaussian Floes there are many serial cubes. See this discussion in the FAQ for more details.
When the job finishes there will be two outputs for this Floe:
gau_torscan_output: Dataset with one multiconformer molecule (one conformer for each torsion increment)
Gaussian Torsion Scan Report: Floe report summarizing torsion scan results (Collection)
Navigate to the Floe Report tab to see the final torsion scan:
The first page of the Floe report for any torsion scan Floe will show all torsions scanned during the job. In this case there is only one molecule, with the torsion highlighted in green.
The plot shows the torsion scan results with angle on the x-axis (in degrees) and relative energy on the y-axis. The orange cirles line shows the relative energy from the force field torsion scan, which includes a Poisson-Boltzman solvent model (MMFF/PB Energy). The Green triangle line shows the Gaussian results. The orange vertical line (around 285 degrees) indicates the angle of this torsion in the reference dataset.