Simple NEB

Cyclohexane - Reaction path:

In this tutorial, we will use NEB to find pathways for the chair ↔ twist-boat isomerization of cyclohexane using an OPLS-AA MM energy model. The stable chair and twist-boat conformations of cyclohexane have previously been determined by geometry optimization.

• Step1 – Start a new project and load the files to the system:

a) On the main menu go to File -> New.

b) On the separate window select System Type to OPLS.

c) Change the working folder to the one of your choice.

d) Load the cyclohexane chair conformation file.

e) Now right click the new system header and click "Import Data".

f) On the separate window select "xyz - simple coordinate file" as your file and load the cyclohexane twisted boat file.

• Step 2 – Running Nudge Elastic Band (NEB):

NEB is a technique to determine reaction paths, using MM, QC or hybrid methods. Such method only requires the initial and final structures.

a) On the main menu, click on Simulate then Running Nudge Elastic Band (NEB).

b) On the popup window select the chair configuration as Reactants and the twisted boat configuration as Products then hit Run.

• Step 3 – Checking Results:

a) In the system header, right-click then select the option "Import Data".

b) Change the format to "pkl folder – pDynamo trajectory" and select the folder generated by the NEB.

c) On the main menu, select Analysis then PES Analysis.