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ORCA quantum chemistry integration

molchanica integrates with the ORCA quantum chemistry software. It provides powerful tools which can supplement this application's functionality. We only support a targeted subset of Orca's functionality, and provide a simple UI for this. This documentation page provides a practical description; for details on how these computations are performed, and hints on how to configure the Orca run, reference the official ORCA manual.

To use, first mark the ORCA toolbar as visible in the UI. If it detects that ORCA is installed and on the system path, you will see a green ORCA ready label on the left of the ORCA toolbar. If not, you will see ORCA unavail, and the Run button will be hidden.

Orca's computations are performed on the active molecule, i.e. selected with right click, or by clicking its associated UI entry. It works best for small molecules, and is too computationally intense for most proteins. Compared to other functionality in this application, ORCA is very slow.

Warning: ORCA computations are currently blocking, and prevent other use of the program while running. We will change this in a future version.

Tasks

To select which functionality to use ORCA for, use the Tasks dropdown in the ORCA toolbar. This selects the primary mode of operation, and determines how ORCA's output will affect the active molecule. Controls specific to a given task appear to the right of this, if applicable.

Calculate single point energy

This computes the single point energy, and other properties of the system, including Mulliken charges.

Example ORCA input generated:

!HF-3c

* xyz 0 1
N      -3.58420     -0.45940      0.12010
C      -2.22280     -0.17670     -0.34410
C      -1.22390     -0.45710      0.79330

Optimize molecule geometry

ORCA geometry optimization example

This adjusts atom positions

Example ORCA input generated:

!r2SCAN-3c TightOpt

* xyz 0 1
N      -3.58420     -0.45940      0.12010
C      -2.22280     -0.17670     -0.34410
C      -1.22390     -0.45710      0.79330

Assign MBIS partial charges to atoms

ORCA MBIS charges example

This computes Minimal Basis Iterative Stockholder (MBIS) partial charges for each atom. When complete, this updates charges on each atom in-place. You can then save the result to file (SDF, Mol2 etc), and run molecular dynamics using these charges. These charges are more accurate than the ones we compute by default, but take a long time to compute.

Example ORCA input generated:

!PBE0 D4 def2-TZVP MBIS

* xyz 0 1
N      -3.58420     -0.45940      0.12010
C      -2.22280     -0.17670     -0.34410
C      -1.22390     -0.45710      0.79330

Perform ab-initio molecular dynamics

This performs molecules dynamics, and creates a set of snapshots (aka trajectories) which can be viewed or saved, using the same system as our native classical MD simulation. Output trajectories are parsed from the XYZ files produced by ORCA. MD parameters are taken from this application's standard MD configuration when applicable: This includes target temperature, thermostat configuration, dt, and number of steps.

Example ORCA input generated:

!r2SCAN-3c %md
    Timestep 2.0_fs
    Initvel 310.0_K
    Thermostat CSVR 310.0_K Timecon 10.0_fs
    Dump Position Stride 1 Filename "out_traj.xyz"
    Run 100
end

* xyz 0 1
N      -3.58420     -0.45940      0.12010
C      -2.22280     -0.17670     -0.34410
C      -1.22390     -0.45710      0.79330

Choosing a method/functional, and basis set

Orca manual: Basis sets

There are many experimental methods and basis sets to choose from. If you know which you wish to use, select from the drop down. Here are some good defaults for use with small organic molecules. Composite methods (Ones with a -3c suffix) are convenient, efficient, and don't require choosing an explicit basis set.

  • r2SCAN-3c: A composite general default for small organic molecules
  • Hf-3C This Hartree Fock composite method is rough, and very fast.
  • PBE0: A reliable general-purpose method
  • def2-TZVP - A good default basis set

Dispersion correction

We recommend enabling the D4 setting when not using a composite (-3c) method; this adds a dispersion correction to the computation.

Running

Click the Run button when ready. This will immediately print the ORCA input generated to the console, and begin the computation. If you're familiar with ORCA, this input will help validate that the computation you expect is being performed, and may be useful for documenting your runs. If not, please contact us with your ORCA workflow so we can improve the UI.

This may time some time. (See the note above about blocking the application) Once complete, the full ORCA output will be displayed in the console, and properties of the active molecule will be updated depending on the task.