DFTB charges, frequencies and dynamics (MD)

This tutorial will walk you through a few features of the DFTB engine, using the GUI. DFTB is computationally much faster than DFT, making it suitable for molecular dynamics evaluations, even on large systems.

We will walk through three different steps in this tutorial. The first step aims at pre-optimizing a simple molecule with DFTB. The second step will evaluate IR frequencies, spectrum and vibrational modes. In the third and last step we will perform a simple molecular dynamics calculation.

Step 1: DFTB: Pre-optimization and Charges

Start ADFjobs
SCM → New Input
Select the DFTB panel: panel bar ADF → DFTB
In the ADFinput panel:
cmd/ctrl-F, find benzene
Select the entry Benzene(ADF) in the Molecule section of the search result
Select the Main panel
Set the model to DFTB
Set the parameter directory to “Dresden” (normally you would want to use better parameters like the included 3ob set)
Move your mouse over the parameter set option, and note the references in the help balloon

Click ‘Pre-optimize’ in the DFTB panel to optimize the molecule

When done (DFTB Ready in the lower left corner of the window) use the View → Atom Info → Atomic charge: Net (dftb) → Show menu command to show the DFTB charges on each atom

A Self Consistent Charge (SCC) evaluation allows atomic Mulliken charges to vary in an iterative procedure. This updates the DFTB Hamiltonian until self consistence of these charges is reached.

Enabling SCC requires higher computational cost due to the iterative procedure taking place for each energy evaluation, but leads to higher accuracy of the final result. If SCC is disabled, the resulting final charges are not self consistent, thus the procedure will be faster, but less accurate.

Set the model to SCC-DFTB
Click ‘Pre-optimize’ again in the DFTB panel to optimize the molecule.

Note how both equilibrium geometry and atomic charges are affected by the SCC evaluation:


Step 2: Frequency evaluation

This example will show how to compute vibrational frequencies and modes using DFTB.

Choose Geometry Optimization as the Task to perform
Choose Followed By → Frequencies
File → Run, use DFTBFrequencies as name when asked for a name
In ADFjobs:
Select the “DFTBFrequencies” job
Click on SCM → Spectra
Click on each individual frequency band to show the associated vibrational mode.

Step 3: Molecular dynamics

In this example, we will perform a simple molecular dynamics calculation using DFTB.

In the ADFinput window, choose MolecularDynamics as the Task to perform.
Choose Followed By → Nothing
Make sure the model SCC-DFTB option is selected, and the parameter set is Dresden (normally you want to use better parameters like the included 3OB set)

Click on the Details button MoreBtn to the right of the Molecular Dynamics task

Set the Number of steps to 2000
Set the Time step to 0.5
set the Sampling frequency to 5
Choose Initial velocities → Random

We now need to set the Thermostat options:

Click on the Details button MoreBtn to the right Thermostat

Select Thermostat → Berendsen
Set the Damping constant to 10 fs
Set the Temperature to 500.0 kelvin

Save your input choosing File → Save as ..., with name “DFTB-MD”
File → run

You can monitor the calculation in real-time:

While the calculation is running: SCM → Movie