This repository contains different CP2K tutorials (originally developed for other softwares) for simulating biochemical processes.

Description: Several QM/MM tutorials adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD.

Author: Salomé Llabrés Prat, PhD

Dependencies:

• Ambertools
• Visualisation tools: Pymol or VMD.
• Python3 and jupyter notebook
• CP2K (v.6) (compiled with plumed plugin)

Tutorial developed by Dr. Ross Walker for the AMBER 15 software. The goal of the tutorial is to do fast and accurate coupled potential semi-empirical QM/MM simulations with full treatment of long range electrostatics (PME) or Generalized Born implicit solvent simulations using a simple toy system.

Reference: http://ambermd.org/tutorials/advanced/tutorial2/index.htm

Adapted tutorial can be found in the folder: AMBER_NMA

Difficulty level: Basic

Tutorial developed by Dr. Gerrit Groenhof for the GMX. The goal of this tutorial is to set up a QM/MM simulations that reproduce a Diels-Alder reaction in different environmnts: in vacuum, in solution and in complex with the protein.

Reference: http://wwwuser.gwdg.de/%7Eggroenh/EMBO2004/html/introduction.html

Adapted tutorial can be found in the folder: GMX_DAA

Difficulty level: Basic

Notes Issues reported on Section 1 and Section 2.