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: Build the initial and final molecule

Start ADFinput
Build the chloromethane molecule using the search function
Add the chloride on the other side
Set the Cl-C-Cl angle to 180 degrees
Set the distance between C and the new chloride to 400 pm
Select the carbon atom
Set the carbon as the origin: Edit → Set Origin
/scm-uploads/doc.2016/Tutorials/_images/t15-initial.png

This will be our initial system, and we will use it as a template for our final system. It is important that atoms are ordered the same in the initial and final molecule. We achieve this by copying and pasting the initial molecule.

Select all the atoms
Copy the selection
Add a new molecule: Edit → New Molecule
Paste the molecule

You can switch between the molecules and rename them using the buttons at the bottom. The second molecule will be the final system. We cannot mirror the whole molecules, because the same chloride will remain bonded. Let us modify the system.

Select the methyl group
Mirror the methyl group about the XY-plane: Edit → Mirror → XY-Plane
Set the carbon as the origin
Remove the bond between the methyl and the chloride
Set the distance between C and the chloride to 400 pm
Add a bond between the methyl and the other chloride
/scm-uploads/doc.2016/Tutorials/_images/t15-final.png

Step 2: Set the calculation details

Now we will set the calculation details.

Select the “Transition State Search - NEB via ASE” preset
Set the Total charge to -1
Click on the ”...” button next to the TransitionStateNEBiaASE task to go to the ‘Nudged Elastic Band’ panel
/scm-uploads/doc.2016/Tutorials/_images/t15-neboptions.png

Some of the options in this panel are used when doing the NEB calculation with only ADF. The default value of the spring constant is fine. For this tutorial set the number of images to 3. Normally one would use the default (8) or bigger. However, then the calculations would take too much time for a tutorial. The ASE only options should be left checked on as well. The initial and final button allow you to switch between the molecules, and create them if you did not already.

Click on the Details tab and select “Geometry Convergence”

The convergence criteria can be entered here. The default values will do.

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 plotted versus the reaction coordinate
/scm-uploads/doc.2016/Tutorials/_images/t15-tsmovie.png