Open source software for enhanced-sampling simulations
Location : CECAM-Lugano, Lugano, Switzerland
July 22, 2019 – July 27, 2019
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.
Vojtech Spiwok (University of Chemistry and Technology, Prague)
Elena Papaleo (Danish Cancer Society Research Center – Denmark)
Alessandro Barducci (Centre de Biochimie Structurale )
Jérôme Hénin (CNRS, IBPC)
Fabio Pietrucci (Sorbonne Université)
Omar Valsson (Max Planck Institute for Polymer Research)
Toni Giorgino (Consiglio Nazionale delle Ricerche)
Ensing Bernd (University of Amsterdam)
Lucie Delemotte (KTH Science for Life Laboratory)
Michele Ceriotti (Swiss Federal Institutes of Technology Lausanne (EPFL))
Michele Parrinello (Swiss Federal Institute of Technology Zurich, Lugano)
Davide Branduardi (Schödinger, Inc)
Francesco Luigi Gervasio (University College London)
Matteo Salvalaglio (University College London)
Michele Vendruscolo (University of Cambridge)
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)