Hybrid Quantum Mechanics / Molecular Mechanics (QM/MM) Approaches to Biochemistry and Beyond

registeration: https://www.cecam.org/workshop-0-1477.html

Day 1 -  May, 15th 2017

Opening. Introduction to QM/MM

• 09:15 to 09:30 - Welcome and Introduction

• 09:30 to 10:15 - Carme Rovira
  

  How to set-up a QM/MM system and why using a QM/MM approach: From pristine crystallographic coordinates to the setup for dynamical simulations. Part I

  
  

• 10:15 to 10:45 - Mauro Boero
  

  Practical aspects: size of the QM region, initial structure (classical equilibration), QM/MM protocol; computational requirements

  
  

• 10:45 to 11:15 - Coffee Break

• 11:15 to 12:00 - Carme Rovira
  

  Basic usage of QM/MM in CPMD

  
  

• 12:00 to 12:30 - Flash Presentation

• 12:30 to 13:30 - Lunch

• 14:00 to 18:00 - Exercises

• 18:00 to 19:30 - Poster Session with cold buffet sandwiches

Day 2 -  May, 16th 2017

Connection between the QM and MM subsystems

• 09:00 to 09:45 - Mauro Boero
  

  Partitioning the system: QM/MM Hamiltonian and calculation of forces

  
  

• 09:45 to 10:30 - Carme Rovira
  

  How to set-up a QM/MM system and why using a QM/MM approach: From pristine crystallographic coordinates to the setup for dynamical simulations. Part II

  
  

• 10:30 to 11:00 - Coffee Break

• 11:00 to 11:45 - Mauro Boero
  

  QM/MM border: link atoms (LA), frontier orbitals (FO), optimized effective core potentials (OECP), scaled-position link atom method (SPLAM)

  
  

• 11:45 to 12:30 - Ursula Roethlisberger
  

  Interactions between the QM and MM subsystems: restrained electrostatic potential (RESP), polarized-boundary redistributed charge (PBRC) and dipole (PBRCD)

  
  

• 12:30 to 14:00 - Lunch

• 14:00 to 18:30 - Exercises

Day 3 -  May, 17th 2017

Dynamics in the QM/MM environment

• 09:00 to 09:45 - Ari Paavo Seitsonen
  

  Molecular dynamics within QM/MM: crucial parameters controlling the dynamics

  
  

• 09:45 to 10:30 - Ari Paavo Seitsonen
  

  Numerical integration schemes for the equations of motion, constants of motion, control of stability, accuracy

  
  

• 10:30 to 11:00 - Coffee Break

• 11:00 to 11:45 - Ursula Roethlisberger
  

  Advanced techniques: Enhanced sampling techniques specially for QM/MM simulations (QM/MM multiple time step, classical bias potentials, CAFES)

  
  

• 11:45 to 12:30 - Mauro Boero
  

  Advanced techniques: Combining QM/MM with Blue Moon ensemble, metadynamics etc I

  
  

• 12:30 to 14:00 - Lunch

• 14:00 to 18:30 - Exercises

Day 4 -  May, 18th 2017

QM/MM with CP2K

• 09:00 to 09:45 - Marcella Iannuzzi
  

  CP2K-QM/MM: Real space multigrid QM/MM implementation

  
  

• 09:45 to 10:30 - Marcella Iannuzzi
  

  Efficient treatment of long-range interactions in a QM/MM scheme

  
  

• 10:30 to 11:00 - Coffee Break

• 11:00 to 11:45 - Mauro Boero
  

  Advanced techniques: Combining QM/MM with Blue Moon ensemble, metadynamics etc II

  
  

• 11:45 to 12:30 - Pablo Campomanes
  

  Basic usage of QM/MM in CP2K

  
  

• 12:30 to 14:00 - Lunch

• 14:00 to 18:30 - Exercises

• 19:30 to 22:00 - Social Dinner

Day 5 -  May, 19th 2017

Advanced techniques

• 09:00 to 09:45 - Pablo Campomanes
  

  Advanced techniques: Recent applications of QM/MM methods

  
  

• 09:45 to 10:30 - Ari Paavo Seitsonen
  

  Advanced techniques: van der Waals interactions, nuclear quantum effects within DFT-based simulations

  
  

• 10:30 to 11:00 - Coffee Break

• 11:00 to 12:00 - Ivano Tavernelli
  

  Advanced techniques: Combining QM/MM with TD-DFT

  
  

• 12:00 to 13:30 - Lunch

• 13:30 to 17:00 - Exercises

Organisers

• Carme Rovira (University of Barcelona, Spain)

• Mauro Boero (University of Strasbourg and CNRS - IPCMS, France)

• Ari Paavo Seitsonen (Ecole Normale Supérieure, France)

• Ursula Roethlisberger (Swiss Federal Institute of Technology Lausanne (EPFL), Switzerland)

Supports

  MARVEL

  CECAM

Description

The scope of the present School, which follows previous editions held in 2011, 2013 and 2015, is to present the main features of quantum mechanics/molecular mechanics (QM/MM) approaches for simulating biomolecular systems, as well as the particularities of different currently available QM/MM computer codes. In this School, special emphasis will be given to advantages and disadvantages, practical applications and new advanced techniques aimed at exploring the terrain beyond simple static relaxations and standard molecular dynamics simulations. The main goal will be to provide to neophytes a solid background to enable them to simulate complex systems of biological, medical and environmental relevance. See the attached appendix file for further details.

The explicit objectives of the present tutorial will be to provide to attendants a paradigm to follow to start and conduct typical QM/MM simulations. Specifically:
• Preparation and pre-equilibration of a biochemical system prior to any QM approach and QM/MM partitioning. We will illustrate with specific examples how to choose the starting system and how to perform a classical molecular dynamics pre-run.
• The problem of the solvent. Experimental crystallographic data generally provide only the coordinates of the non-hydrogen atoms of protein/nucleic acid and in some cases their counter-ions and a few water molecules, if at all. We will discuss how to add the missing hydrogen atoms and how to include the solvent, an essential element of biochemical systems both in in vivo and in vitro environments. Then we shall show some guidelines about how to selec those water molecules that undergo chemical reactions and, hence, cannot be treated at a classical level.
• We shall discuss different methods to setup covalent boundaries between the two subsystems, QM and MM (link atoms, frontier orbitals, optimized effective core potentials, scaled-position link atom method, etc.) with their advantages and drawbacks.
• Important parameters to be selected and controlled before and during the simulation by the user.
• Time scale problem of QM/MM simulations, performance and stability of QM/MM dynamical simulations and accuracy of such a description and arbitrary partitioning of a large complex biological system.

There is no registration fee for this tutorial. Accommodation is covered for all accepted applications.