Reaction path and TS search using NEB¶

Start AMSjobs

1. in the menu bar select SCM → New input

This will open a new AMSinput window.

In AMSinput:

1. Switch to the DFTB panel: →

2. Select Task → NEB

We will use the GFN1-xTB model, which is the default model as of the AMS2020 release. Your AMSinput window should look like this:

When setting up an NEB calculation we need to specify two systems: the initial and final states of the reaction. The NEB algorithm will then generate a set of images by interpolating between the initial and final systems. This will be the initial approximation of the reaction path, which will be optimized during the NEB calculation.

1. Download the following xyz files: file NEB_initial.xyz and NEB_final.xyz

2. Import the coordinates of the initial system: in the menu bar, select File → Import Coordinates… and select the file NEB_initial.xyz

3. Create a new molecule-tab: in the menu bar, select Edit → New Molecule…

4. Import the coordinates of the final system in the newly created molecule tab: in the menu bar, select File → Import Coordinates… and select the file NEB_final.xyz

You can switch between the two molecule tabs by clicking arrows at the bottom of the molecule drawing area.

Now, go to the NEB details panel where we will set up the NEB calculation:

1. Click on next to Task → NEB to go to the NEB details panel

2. From the drop-down menu next to initial system, select Mol-1

3. From the drop-down menu next to final system, select Mol-2

4. Check the Characterize PES point checkbox

Your AMSinput window should look like this:

We are now ready to run the calculation:

In AMSinput:

1. In the menu bar, click on File → Save and give it the name “NEB_tutorial”

2. In the menu bar, click on File → Run . This will bring the AMSjobs window to the front

3. Wait for the calculation to finish. It should take just a few seconds

In the logfile you can monitor the progress of your NEB calculation:

In AMSjobs:

1. Select the job “NEB_tutorial” and in the menu bar click on SCM → Logfile. This will open the logfile

A NEB calculation consists of several steps, which are automatically executed one after the other:

• first, the two end points (the initial and final molecules) are optimized (in the logfile, look for Optimizing initial state and Optimizing final state)

• then the NEB reaction path will be optimized (in the logfile, look for NEB Path Optimization). During the reaction path optimization, the highest-energy image on the path will climb to the transition state

• finally, a single point calculation for the TS is performed (in the logfile: Final calculation for highest-energy image). If the option Characterize PES point is on, then the lowest-lying normal modes will be calculated in order to validate the TS (the TS should have exactly one imaginary frequency). Some information on the reaction path is printed at the end of the logfile:

  NEB found a transition state!
  TS barrier height from the left           0.02576078 Hartree
                                           16.165 kcal/mol
                                           67.635 kJ/mol
  TS barrier height from the right          0.08632064 Hartree
                                           54.167 kcal/mol
                                          226.635 kJ/mol
  

Now, let’s visualize the reaction path computed by NEB:

In AMSjobs:

1. Select the job “NEB_tutorial” and, in the menu bar, click on SCM → Movie. This will open the AMSmovie module

In AMSmovie, you can click on play (or drag the slide-bar) so see the reaction happening. On right-hand side, the energy and gradients of the images in the NEB reaction path are plotted.

The transition state is characterized by having one imaginary frequency. Let’s visualize the normal modes of the transition state geometry with AMSspectra:

In AMSmovie:

1. click on SCM → Spectra. This will open the AMSspectra

Here you will see the computed normal modes for the TS geometry. Notice that there is one negative frequency (imaginary frequency are shown as negative numbers).

In AMSspectra:

1. In the table, click on the line with the negative frequency

The corresponding normal mode will be displayed in the molecule-visualization area. This normal mode gives you an idea of how the atoms are moving as they cross the transition state.