cp2K_qmmm_tutorials_for_biological_simulations

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cp2K_qmmm_tutorials_for_biological_simulations

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Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.

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# 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](http://ambermd.org/AmberTools.php)
- Visualisation tools: [Pymol](https://sourceforge.net/projects/pymol/) or VMD.
- Python3 and jupyter notebook
- CP2K (v.6) (compiled with plumed plugin)

---

## 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](http://ambermd.org). 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](http://www.gromacs.org/Documentation/Tutorials). 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.

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