CP2K_tutorials

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)

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Original tutorials:

Tutorial from the AMBER suite

1. Comparison of N-methylacetamide conformation between Classical MD and QM/MM/MD simulations

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

Tutorials from the GMX community

1. Diels-Alder Antibody Catalyst (DAA)

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.