Rowan Docs

Submitting a Scan

Running a scan will give you information about the energetic profile of a selected coordinate by running a series of component optimizations (called "scan points"). Rowan uses the wavefront propogation method to run scans, which helps ensure scan points don't get stuck at unfavorable local minima.

To run a new scan, find your way to this screen in Rowan:

Rowan's workflow selection page

If you're currently viewing a calculation or workflow you already ran, hit the "X" icon in the top left of your screen, just below the navigation bar.

To start submitting a scan, click "Scan."

Select a molecule

Scans in Rowan are run on molecules (or systems of molecules). You can either create a structure using Rowan's 2D or 3D editors, or upload a molecule.

To add a molecule, you can use any of the following input formats:

  • Draw a molecule using Rowan's 2D or 3D editors.
  • Upload a file, using the "Upload files" button. (Rowan accepts .xyz, .gjf, .out, .mol2, .sdf, .cif, and .mae chemical file formats.)
  • Paste XYZ coordinates, using the "Paste XYZ" button.
  • Input a SMILES string, using the "Input SMILES" button.
  • Input the name of the chemical, for its information to be fetched from PubChem.
  • Drag and drop files anywhere on the page.

For small molecules, it's often easiest to start with a SMILES string. Many 2D molecule drawing programs, including ChemDraw and MarvinJS, will let you export/copy structures as SMILES.

Editing structures

To modify a structure you've already input, you can click the pencil icon in the top right corner of the molecule viewer to use Rowan's 3D editor.

Charge and multiplicity

Make sure to set the appropriate charge and spin multiplicity for your selected molecule.

Level of theory

Select the level of theory you'd like to run your scan at by choosing an appropriate method and basis set.

Rowan won't let you submit a scan with an incomplete basis set for the molecules you've input.

If any input field shows red, hover over it and read the text that will appear for information about the error.

Corrections

If the engine and method you've selected supports it, use the dropdown to select a correction (currently, Rowan only supports the D3BJ and D4 corrections).

Solvent

If the engine and method you've selected supports it, click on the solvent field to select a solvent model and solvent.

Select the scan coordinate

With Rowan, you can scan across the length of a bond between two atoms, the angle created by three atoms, or the dihedral angle between four atoms.

You can manually select the coordinate type and input atom indices, or you can click into the scan coordinate box to select the atoms you want to scan on the 3D viewer.

Once you've selected a coordinate, you'll need to select values for:

  • Start: the smallest value of the selected coordinate to run
  • Stop: the largest value of the selected coordinate to run
  • Num steps: the number of scan points to run

The scan will run its first optimization at the starting coordinate, and do as many steps as you selected to get to the stop coordinate. For example, if you're scanning the bond distance C1–C2 and select start as 1 Å, stop as 2 Å, and num steps as 5, the scan will run an optimization when the C1–C2 bond is 1 Å, 1.25 Å, 1.5 Å, 1.75 Å, and 2 Å.

You can create additional scan coordinates by clicking the "Add coordinate" button. If two scan coordinates share a scan dimension, their scan coordinates will be stepped at the same time.

If you would like to create additional scan dimensions, click the "Add second scan dimension" button. A new box will appear, where you can specify any new scan coordinates. Rowan currently supports a maximum of 2 scan dimensions.

Adding constraints (optional)

If you want to constrain a bond length, an angle, or a dihedral angle at each scan point, you can add constraints.

Adding a constraint means the given bond length, angle, or dihedral angle won't change during the geometry optimization process.

To add a constraint, click "Add new constraint" at the bottom of the new scan page. Select the type of coordinate you'd like to constrain and input the appropriate indices. You can also select the atoms using the molecule viewer by first selecting the constraint row and then clicking on the atoms.

Be sure to input the right indices in the right order, otherwise you'll get unexpected results. (Angle A–B–C is not equivalent to angle B–A–C!)

Submit