CECAM

Open source software for enhanced-sampling simulations

Location : CECAM-Lugano, Lugano, Switzerland
July 22, 2019 – July 27, 2019

Organizers:

  • Carlo Camilloni
    University of Milano, Italy
  • Massimiliano Bonomi
    Institut Pasteur – CNRS, France
  • Giovanni Bussi 
    Scuola Internazionale Superiore di Studi Avanzati (SISSA), Italy
  • Gareth Tribello
    Queen’s University Belfast, United Kingdom

   

Molecular dynamics (MD) simulations allow complex phenomena to be studied at a unique spatial and temporal resolution. While conventional simulations provide insights into processes that occur on short time scales, the study of rare events such as protein folding, chemical reactions and phase transitions remains prohibitive in many cases of interest. To extend the time scale that is accessible in MD, several enhanced-sampling methods have been developed over the years.

Along with such developments, there is a growing need for open-source software that enables the use of enhanced-sampling methods in combination with a variety of different MD codes, which are tailored for specific disciplines. In recent years, a few groups have made an effort to create interoperable, open source software, such as the PLUMED library, the COLVAR module and the SSAGES suite for advanced general ensemble simulations.

The goals of this school are to:
1) train students to use open source software for enhanced-sampling simulations across different disciplines;
2) put in contact end users with developers of enhanced-sampling methods and software to discuss the needs of the community, encourage the development of analysis tools, benchmarks and sharing protocols, promote reproducibility, and ultimately drive future developments of software for enhanced simulations.

The school will be organized into two different parts:
1) a 3-days tutorial that will involve lectures and hands-on sessions using the open source PLUMED library and the GROMACS, LAMMPS and CP2K codes. These codes are typically used for applications that are relevant to biology, condensed/soft matter and chemistry. They are not limited only to these areas, however. 
2) a 3-days workshop in which the developers of various open source software packages for enhanced sampling and the developers and users of these enhanced-sampling methods will participate.

IMPORTANT: when applying, please specify if you are interested in attending both the tutorial and workshop or only the workshop part of the school. For the tutorial, priority will be given to young researchers with little or no experience in the use of enhanced-sampling methods.

There is no registration fee, CECAM will cover housing expenses for students participating to the tutorial and workshop, while workshop only participants will need to cover their own expenses.

The registration deadline is on May 1st. After that day we will contact all applicants.

Topics and objectives of the Tutorial. During the 3-days tutorial we will cover:
– review of the statistical mechanical theory that underlies all free-energy methods;
– review of prominent free-energy methods, with focus on those based on the use of collective variables. In particular, we will review metadynamics, umbrella sampling, steered MD and replica-exchange methods;
– hands-on: calculation of the free-energy surface for realistic systems in the fields of biomolecular dynamics, chemical reactions, and condensed/soft-matter using GROMACS, CP2K, and LAMMPS in combination with PLUMED;
– hands-on: thorough analysis of the results of free-energy calculations (convergence, visualization of free-energy surfaces, error analysis).

The overall objectives of the tutorial are to:
– present prominent free-energy calculation methods to young researchers, with examples of simple applications;
– train the participants on how to use PLUMED with popular MD codes;
– train the participants to perform realistic free-energy calculations tailored to their specific scientific problems;
– train the participants to critically assess the accuracy and reliability of their results (error estimation, comparison of different collective variables and free-energy methods);
– promote the reproducibility of scientific results by using open-source software and sharing protocols and scripts.

Topics and objectives of the Workshop. The 3-days workshop will consist of:
– 18 invited talks from world-leading scientists working in the development of open source software for enhanced-sampling simulations as well as developers and users of enhanced-sampling methods in the field of chemistry, computational biology, and condensed/soft-matter physics;
– 8 contributed talks selected from the abstracts sent by participants;
– 2 panel discussions in which the invited speakers and attendees will participate;
– 1 poster session for participants at the tutorial and workshop.

The overall objectives of the workshop are to:
– showcase how different enhanced-sampling techniques have been applied in real-case scenarios across multiple disciplines;
– highlight common and specific challenges in the application of enhanced-sampling techniques in different disciplines;
– foster discussions among end users and developers of enhanced sampling methods as well as software developers;
– highlight future challenges in developing and distributing open source software and protocols for enhanced-sampling simulations.

Czech Republic

Vojtech Spiwok (University of Chemistry and Technology, Prague)

Denmark

Elena Papaleo (Danish Cancer Society Research Center – Denmark)

France

Alessandro Barducci (Centre de Biochimie Structurale )
Jérôme Hénin (CNRS, IBPC)
Fabio Pietrucci (Sorbonne Université)

Germany

Omar Valsson (Max Planck Institute for Polymer Research)

Italy

Toni Giorgino (Consiglio Nazionale delle Ricerche)

The Netherlands

Ensing Bernd (University of Amsterdam)

Sweden

Lucie Delemotte (KTH Science for Life Laboratory)

Switzerland

Michele Ceriotti (Swiss Federal Institutes of Technology Lausanne (EPFL))
Michele Parrinello (Swiss Federal Institute of Technology Zurich, Lugano)

United Kingdom

Davide Branduardi (Schödinger, Inc)
Francesco Luigi Gervasio (University College London)
Matteo Salvalaglio (University College London)
Michele Vendruscolo (University of Cambridge)

USA

Juan J de Pablo (University of Chicago)
Marta Filizola (Icahn School of Medicine)
Glen Hocky (New York University)
Jim Pfaendtner (University of Washington)
Michael Shirts (U. of Colorado)

Program

 

Tutorial

Monday 22 July 2019 – Day 1

·       9h00 – 9h15

Welcome Massimiliano BONOMI, Giovanni BUSSI

   Carlo CAMILLONI, Gareth TRIBELLO

·       9h15 – 10h30 Lecture 1: Introduction to rare events and collective variables Gareth TRIBELLO

Basics of enhanced sampling methods for chemistry, computational biology and condensed matter physics

·       10h30 – 11h00

Coffee break

  

·       11h00 – 12h30 Lecture 2: Importance sampling – Carlo CAMILLONI

General principles of enhanced-sampling methods based on bias potentials

·       12h30 – 14h00

Lunch break

  

·       14h00 – 16h00 Hands-on 1: Intro to PLUMED syntax – Massimiliano BONOMI

Introduction to the PLUMED package

·       16h30 – 18h30 Hands-on 2: Umbrella sampling – Carlo CAMILLONI

Exercises with umbrella sampling in biology, chemistry, and condensed matter

Tuesday 23 July 2019 – Day 2

·       9h00 – 10h30 Lecture 3: Metadynamics – Massimiliano BONOMI

Theory of metadynamics

·       10h30 – 11h00

Coffee break

  

·       11h00 – 12h30 Lecture 4: Error analysis – Giovanni BUSSI

Theory of error analysis in MD

·       12h30-14h00

Lunch break

  

·       14h00 – 16h00 Hands-on 3: Metadynamics – Giovanni BUSSI

Exercises with metadynamics in biology, chemistry, and condensed matter

·       16h30 – 18h30 Hands-on 4: Errors – Gareth TRIBELLO

Exercises on error analysis

    

 

Wednesday 24 July 2019 – Day 3

·       9h00 – 10h30 Lecture 5: Dimensionality Reduction – Gareth TRIBELLO

Theory of dimensionality reduction

·       10h30 – 11h00

Coffee break

  

·       11h00 – 12h30 Hands-on 5: Dimensionality Reduction – Gareth TRIBELLO

Exercises with dimensionality reduction

·       12h30 – 14h00

Lunch break

  

·       14h00 – 18h00 Hands-on 6: Real-life applications – Massimiliano BONOMI, Giovanni BUSSI,  Carlo CAMILLONI

Large conformational changes in proteins (GROMACS), chemical reactions (CP2K), phase transitions (LAMMPS)

 

 

Workshop

Thursday 25 July 2019 – Day 1

 

·       8h30 – 9h30

Registration

 

·       9h30 – 10h00

Michele Vendruscolo

 

·       10h00 – 10h30

Lucie Delemotte

 

·       10h30 – 11h00

Coffee break

 

·       11h00 – 11h30

Juan J De Pablo

 

·       11h30 – 12h00

Jérôme Hénin

 

·       12h00 – 12h30

Presentation from CSCS

 

·       12h30 – 12h45

Paul Robustelli (contributed)

 

·       12h45 – 14h00

Lunch break

 

·       14h00 – 14h30

Marta Filizola

 

·       14h30 – 15h00

Michele Ceriotti

 

·       15h00 – 15h30

Davide Branduardi

 

·       15h30 – 16h00

Coffee break

 

·       16h00 – 17h30

Discussion 1

 

Developing open source and interoperable software for enhanced-sampling simulations: challenges and opportunities. We will discuss the importance of sharing methods and protocols within and across disciplines as well as how to promote reproducibility and the crucial role that open, interoperable, and community-driven software plays in achieving these goals.

 

·       17:30 – 19:00

Poster session

 

 

 

Friday  26 July 2019 – Day 2

 

 

·       9h00 – 9h30

Michele Parrinello

 

 

·       9h30 – 10h00

Michael Shirts

 

 

·       10h00 – 10h30

Toni Giorgino

 

 

·       10h30 – 11h00

Coffee break

 

 

·       11h00 – 11h30

Jim Pfaendtner

 

 

·       11h30 – 12h00

Matteo Salvalaglio

 

 

·       12h00 – 12h15

Davide Donadio (contributed)

  

·       12h15 – 12h30

Daniela Polino (contributed)

  

·       12h30 – 14h30

Lunch break

 

 

·       14h30 – 15h00

Elena Papaleo

 

 

·       15h00 – 15h30

Glen Hocky

 

 

·       15h30 – 16h00

Coffee break

 

 

·       16h00 – 16h30

Bernd Ensing

 

 

·       16h30 – 17h00

Omar Valsson

 

 

·       17h00 – 17h15

Yong Wang (contributed)

  

·       17h15 – 17h30

Riccardo Capelli (contributed)

  

·       17h30 – 19h00

Discussion 2

  

Challenges in applying enhanced-sampling methods across different disciplines: benchmarking and sharing 

 
       

 

Saturday 27 July 2019 – Day 3

 

·       9h00 – 9h30

Vojtech Spiwok

 

·       9h30 – 10h00

Alessandro Barducci

 

·       10h00 – 10h30

Break

 

·       10h30 – 11h00

Francesco Gervasio

 

·       11h00 – 11h30

Fabio Pietrucci

 

·       11h30 – 11h45

Michele Invernizzi (contributed)

 

·       11h45 – 12h00

Conrado Pedebos (contributed)