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

1. Start ADFjobs
2. SCM → New Input
3. Select the DFTB panel: ADFPanel → DFTBPanel

4. Open the search box by pressing cmd/ctrl-F or by clicking the magnifying glass, type benzene.
5. Select the entry Benzene(ADF) in the Molecule section of the search result
6. Set the Model to DFTB
7. Set the Parameter directory to Dresden
8. Move your mouse over the parameter set option, and note the references in the help balloon

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

10. 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
../_images/t12_DFTBnoscccharges.png

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.

1. Set the Model to SCC-DFTB
2. 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:

../_images/t12_DFTBcharges.png

Step 2: Frequency evaluation

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

1. Make sure the Task is set to Geometry Optimization
2. Tick the Frequencies check-box
../_images/t12_freqinput.png
1. File → Run, use DFTBFrequencies as name when asked for a name
2. The ADFjobs window should come to the front as the job starts running
3. Select the DFTBFrequencies job
4. Click on SCM → Spectra
5. Click on each individual frequency band to show the associated vibrational mode
../_images/t12_spectra.png

Step 3: Molecular dynamics

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

1. In the ADFinput window, choose MolecularDynamics as the Task to perform.
2. Untick the Frequencies check-box
3. Make sure the model SCC-DFTB option is selected, and the parameter set is Dresden

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

5. Set the Number of steps to 2000
6. Set the Time step to 0.5 fs
7. Set the Sampling frequency to 5
../_images/t12_dynamics_input.png

We also want attach a thermostat to the system.

1. Click on the Details button MoreBtn to the right Thermostat
2. Click the + button to add a new thermostat.
3. Select Thermostat → Berendsen
4. Set the Damping constant to 10 fs
5. Set the Temperature to 500 K

6. Save your job via File → Save as …, using the name DFTB-MD
../_images/t12_thermostat_input.png
1. Save your job via File → Save as …, using the name DFTB-MD
2. Start your job by clicking File → Run
3. The ADFjobs window should come to the front as the job starts running

You can monitor the calculation in real-time:

1. While the calculation is running: SCM → Movie
../_images/t12_dynamics_energy.png