Hybrid Quantum Mechanics / Molecular Mechanics (QM/MM) Approaches to Biochemistry and Beyond
- 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)
Now on-line broadcast:
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.
Registration deadline: March 28