/**
\page lugano-6c Lugano tutorial: Computing proton transfer in water

\section lugano-6c-aim Aims

In this tutorial I will show you how you can use PLUMED and metadynamics in combinations with CP2K.

\section lugano-6c-lo Objectives

Once this tutorial is completed students will

- Know how to enhance the sampling in an ab initio simulation.

\section lugano-6c-resources Resources

The \tarball{lugano-6c} for this project contains the following files:

- H-transfer.inp: a CP2K input file to perform BO-MD and Free Energy calculations with PLUMED
- H-transfer.pdb: a PDB file with the starting configuration for a few water molecules

This tutorial has been tested on v2.5 but it should also work with other versions of PLUMED.

\section lugano-6c-intro Introduction

For this tutorial we will consider a practical application. The aim is that of studying proton transfer in water. 
The system is simplified and the accuracy of the ab initio simulation is not production like so do not reuse the
CP2K input for real-life applications.

\section lugano-6c-exercises Exercises

In this example the system is initially in a configuration where there are H3O+ and an OH- molecule separated by a few
other water molecules. In a standard MD the system will quickly equilibrate. Here the aim is to use metadynamics to estimate
the free energy of this process and to understand the role of the solvent. 

When you download CP2K it already includes the interface for PLUMED but it must be compiled using the proper flags, check CP2K installation instructions.


\section lugano-6c-ex-1 Exercise 1: Preliminary run 

The starting configuration is represented in the H-transfer.pdb. While a simple CP2K input file to perform BO-MD is written in
H-transfer.inp. In particular here the section to enable PLUMED is commented out initially.

\verbatim
# &FREE_ENERGY
#   &METADYN
#     USE_PLUMED .TRUE.
#     PLUMED_INPUT_FILE ./plumed.dat
#   &END METADYN
# &END FREE_ENERGY
\endverbatim

To run a preliminary simulation it is enough to:

\verbatim
cp2k.sopt H-transfer.inp >& log &
\endverbatim

use the plumed \ref driver and VMD to choose to water molecule relatively far apart to study the proton transfer.

\section  lugano-6c-ex-2 Exercise 2: Proton transfer

In this exercise you are challenged to
- Select two water molecule to be kept far apart using \ref LOWER_WALLS and the distance between their two oxygen atoms.
- Use the distances of an hydrogen from both oxygen atoms to setup a first \ref METAD calculation to study the proton transfer between the selected water molecules
- Test more complex CVs maybe taking into account the role of the other molecules.
- Think how to study proton transfer in a general way instead than between two specific water molecules and using a specific hydrogen.

The number of steps in the simulation is initially set to 100, this should be increased so to allow a more extensive exploration of the conformational space.
This simulation can be slow and is better run on a workstation with multiple processors.

*/

link: @subpage lugano-6c 

description: An exercise to run a simple proton transfer calculation with CP2K 

additional-files: lugano-6c
