CECAM

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

The scope of this tutorial, which follows two previous events held in February 2011 and 2013, is to present the main features of quantum mechanics / molecular mechanics (QM/MM) approaches for simulating biomolecular systems. The interest in multiscale approaches that are able to take into account different levels of accuracy in the description of large systems is continuously growing and has been honored by last year’s the Nobel Prize in Chemistry that was jointly awarded to M. Karplus, M. Levitt and A. Warshel. In fact, the combination of quantum mechanics and molecular mechanics (QM/MM), introduced by the seminal work of Warshel and Levitt (J. Mol. Biol. 103, 227, 1976), in combination with the increasing computational power of modern parallel, vector-parallel and hybrid CPU-GPU platforms, has lead to a real breakthrough in the simulations of realistic systems in condensed phases, in particular for the description of biomolecular reactions. The main goal of this tutorial will be to provide to neophytes a solid background to enable them to simulate complex systems of biological, medical and environmental relevance. The tutorial is organized with theoretical lessons and examples of successful (and unsuccessful) simulations, as well as with practical exercises, planned for the afternoon sessions.

Housing for five nights at the Youth Hostel in Lausanne will be provided by CECAM.

There is no registration fee for this tutorial.

Registration deadline has passed, we can no longer accept more participants.

Austria

Patrick Zobel (Institute of Theoretical Chemistry, University of Vienna)

Czech Republic

Mohamed Eldessouki (Technical University of Liberec)
Pavel Janoš (National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno)

Finland

Lauri Himanen (Centre of Excellence in Computational Nanoscience, Aalto University)

France

Burak OZDAMAR (Institut de Physique et Chimie des Matériaux de Strasbourg)

Germany

Xiangyang guo (Martin-Luther-Universität Halle-Wittenberg)
Puneet Gupta (Max Planck Institute for Chemical Energy Conversion)
Kristof Karhan (University of Paderborn)
Narendra Kumar (Ruhr-Universitat Bochum, Germany)
Markus Schneider (Fritz Haber Institute of the MPS)
Xiaoqing Wang (Max Planck Institute for the Physics of Complex System)

Hungary

Tamas Bihari (Research Centre for Natural Sciences, Hungarian Academy of Sciences)

India

Usharani Dandamudi (Department of Lipid Science, CSIR-CFTRI)

Italy

Alejandro Gil Ley (International School for Advanced Studies (SISSA))
Matic Pavlin (CNR-IOM c/o Scuola Internazionale Superiore di Studi Avanzati (SISSA))
Paolo Restuccia (Universita’ degli Studi di Modena e Reggio Emilia)
Silvia Rinaldi (CNR-Institute of Chemistry of Molecular (ICRM), Milano)

The Netherlands

Habiburrahman Zulfikri (University of Twente)

Poland

Pawe³ Wityk (The University of Gdañsk)

Portugal

Adrià Gil-Mestres (Universidade de Lisboa)

Spain

Fedaa Attana (University of Valencia)
Maria Fumanal (Universitat de Barcelona)
Lluís Raich-Armendariz (University of Barcelona)
Adrian Romero (University of Girona)

Switzerland

Luciano Abriata (EPFL)
Assil Bouzid (EPFL )
Pablo Campomanes (University of Fribourg)
Teodoro Laino (IBM Research – Zurich)
Hyungjun Lee (Swiss Federal Institute of Technology Lausanne (EPFL))
Riccardo Petraglia (Swiss Federal Institute of Technology (EPFL))
Ivano Tavernelli (IBM-Zurich Research)

United Kingdom

Victoria Oakes (University of Bath)
Reynier Suardiaz (University of Bristol)

USA

Lorenzo Casalino (University of California, San Diego)

Monday February 9th 2015 – Day 1
Opening; introduction to QM/MM

10:15 to 10:30 – Welcome and Introduction
10:30 to 11:15 – 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
11:15 to 12:00 – Mauro Boero 
Practical aspects: size of the QM region, initial structure (classical equilibration), QM/MM protocol; computational needs
12:00 to 12:30 – Carme Rovira 
Basic usage of QM/MM in CPMD
12:30 to 14:00 – Lunch
14:00 to 18:00 – Exercises
Tuesday February 10th 2015 – Day 2
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 18:00 – Exercises
18:00 to 20:30 – Poster Session with cold buffet sandwiches
Wednesday February 11th 2015 – Day 3
QM/MM with CP2K

09:00 to 09:45 – Mauro Boero 
2nd generation Car-Parrinello in CP2k
09:45 to 10:30 – Ari Paavo Seitsonen 
Treating London dispersion forces/van der Waals interactions with approximate DFT functionals
10:30 to 11:00 – Coffee Break
11:00 to 11:45 – Teodoro Laino 
Real space multigrid QM/MM implementation / Efficient treatment of long-range interactions in a QM/MM scheme
11:45 to 12:30 – 
Basic usage of QM/MM in CP2K
12:30 to 14:00 – Lunch
14:00 to 18:00 – Exercises
Thursday February 12th 2015 – Day 4
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 metadynamics or Blue Moon ensemble I
12:30 to 14:00 – Lunch
14:00 to 18:00 – Exercises
19:30 to 22:00 – Social Dinner
Friday February 13th 2015 – Day 5
Advanced techniques

09:00 to 09:45 – Mauro Boero 
Advanced techniques: Combining QM/MM with metadynamics or Blue Moon ensemble II
09:45 to 10:30 – Pablo Campomanes 
Examples of (successful and unsuccessful) applications II
10:30 to 11:00 – Coffee Break
11:00 to 11:45 – Ivano Tavernelli 
Advanced techniques: Combining QM/MM with TD-DFT
11:45 to 13:00 – Lunch
13:00 to 16:45 – Exercises
16:45 to 17:00 – Closing Word