CECAM School: "Enhanced sampling methods with PLUMED"
|Date||03.07.2023 › 06.07.2023|
|Hour||09:00 › 17:30|
|Category||Conferences - Seminars|
You can apply to participate and find all the relevant information (speakers, abstracts, program,...) on the event website: https://www.cecam.org/workshop-details/1200
Please consult this page before applying: https://github.com/plumed/cecam2023/blob/main/README.md.
Deadline for applications: May 4th 2023.
In recent years, atomistic molecular dynamics (MD) simulations have gained a central role in chemistry, computational biology, and condensed-matter physics. Unfortunately, the large numbers of particles in realistic cases and the complex physico-chemical models that must be used in order to get accurate results make simulations of biomolecules and solid-state materials computationally expensive. As a result, direct MD simulations can only provide insights into processes that occur on relatively short time scales. The study of rare events such as protein folding, drug binding, chemical reactions and phase transitions remains computationally prohibitive in many cases of interest. To extend the time scale accessible in typical MD simulations, several powerful enhanced-sampling methods have been developed over the years. This school will teach students how to run these enhanced-sampling calculations using the open-source PLUMED library (www.plumed.org). The students will be introduced to this area through a series of online classes that they will be expected to complete before the “in-person” school, which will be composed of a two-day hands-on tutorial and a two-day user meeting where presentations on the state of the art will be given.
We have designed this school to be consistent with our conception of PLUMED as a living codebase. We always seek to encourage users to contribute new code to PLUMED so that their methods can be shared with the broadest possible user base via an open-source model. This flexibility has made the code popular, and the PLUMED papers published in 2008, 2014 and 2019 have received 3,652 citations in total. The PLUMED consortium and the PLUMED-NEST repository were introduced in 2019 (www.plumed-nest.org). This consortium currently involves 76 members from 52 different institutions across 17 different countries. This consortium aims to transform the way researchers communicate the protocols used in MD simulations to maximize the impact of new research and promote the highest possible standards of scientific reproducibility. At the heart of this effort is PLUMED-NEST nest, which is a website that users can use to deposit PLUMED inputs that have been used in their un/published simulations. Currently, PLUMED-NEST hosts 198 projects contributed by users and a total of 1212 examples of PLUMED protocols.
 M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Marinelli, F. Pietrucci, R. Broglia, M. Parrinello, Computer Physics Communications, 180, 1961-1972 (2009)
 G. Tribello, M. Bonomi, D. Branduardi, C. Camilloni, G. Bussi, Computer Physics Communications, 185, 604-613 (2014)
 The PLUMED consortium, Nature Methods, 16, 670 (2019)
 G. Bussi, G. Tribello, Analyzing and Biasing Simulations with PLUMED, 2019
 A. Barducci, J. Pfaendtner, M. Bonomi, Tackling Sampling Challenges in Biomolecular Simulations, 2014
 G. Bussi, D. Branduardi, Free-Energy Calculations with Metadynamics: Theory and Practice, 2015
 J. Henin,T. Lelievre, M. R. Shirts, O. Valsson and L. Delmotte, Enhanced sampling methods for molecular dynamics simulations (20222) archive
- Informed public
- Registration required
- Massimiliano Bonomi ( Institut Pasteur - CNRS , France )
Giovanni Bussi ( Scuola Internazionale Superiore di Studi Avanzati , Italy )
Carlo Camilloni ( University of Milano , Italy )
Gareth Tribello ( Queen's University Belfast , United Kingdom )
- Aude Merola-Faillétaz, CECAM Events & Communications Manager