These notebooks explore the proton transfer step associated with the interconversion of the two enol forms of 2-formylcyclohexanone based on DFT calculations. Specifically, the CP2K software package is used together with various Python tools for analysis and visualization.
The hands-on consists of the following parts:
- Part 1: Nudged elastic band (NEB) calculations at PBE level of theory
- Part 2: Vibrational analysis of the transition state
- Part 3: Re-converging the NEB minimum energy profile using the PBE0 hybrid functional
- Part 4: Ab initio molecular dynamics simulation of 2-formylcyclohexanone in aqueous solution
The notebooks are run using Puhti web interface, and they rely on CSC's
cp2k/2024.1 module and a custom Python environment.
- Go to https://www.puhti.csc.fi
- Select Jupyter for courses
- Reservation: sscc_thu_small (applicable during the school)
- Project: project_2006657
- Course module: sscc-2024-cp2k
- Partition: small (default resource settings)
- Launch!