Transition State Search with ASE using the Nudged Elastic Band method

Another way to do a transition state search is using the Nudged Elastic Band method.

This tutorial explains how to setup the calculation to use ASE in combination with ADF. The setup for the native NEB calculation is similar, and only has a few different options in the NEB panel. We will use the SN2 reaction of chloromethane with a chloride ion as an example.

Step 1: Import the initial and final molecule

First, download the initial and final geometry:

Click here to download the .xyz file Chloromethane_TS_initial.xyz
Click here to download the .xyz file Chloromethane_TS_final.xyz
Start ADFinput
Click on File → Import coordinates... and select the file Chloromethane_TS_initial.xyz
Add a new molecule: Edit → New Molecule
Click on File → Import coordinates... and select the file Chloromethane_TS_final.xyz
/scm-uploads/doc.2017/Tutorials/_images/t15-initial.png /scm-uploads/doc.2017/Tutorials/_images/t15-final.png

You can switch between the molecules and rename them using the buttons at the bottom.

Important

It is important that atoms are ordered in the same way in the initial and in the final molecule.

Step 2: Set the calculation details

Now we will set the calculation details.

Set the Total charge to -1
Select the Transition State task
Click the MoreBtn next to the task
Select the ‘ASE-NEB’ method
Click the MoreBtn to go to the ‘Nudged Elastic Band’ panel
Set the number of images to 3
/scm-uploads/doc.2017/Tutorials/_images/t15-neboptions.png

The default value of the spring constant is fine. For this tutorial we use 3 images. Normally one would use the default (8) or bigger. However, then the calculations would take too much time for a tutorial. The initial and final button allow you to switch between the molecules, and create them if you did not already.

Use File → Save As to save the file as ‘SN2_NEB’
Run the calculation

Step 3: Viewing the Results

When the calculation is finished we can take a look at the results. Open ADFmovie.

Use Graph → Energy to display a graph with the energy of the NEB images
/scm-uploads/doc.2017/Tutorials/_images/t15-tsmovie.png