PLUMED Masterclass

PLUMED Masterclass is a series of virtual and interactive classes, each one focused on a specific theme ranging from basic concepts to advanced topics in molecular simulations. Each class is composed by two lectures held on Zoom:

In between the two lectures, the participants will have one week to complete the exercises on their own or in groups. They will have access to a dedicated Slack organization, where they will be able to interact with lecturers and with other participants during the entire week.

Zoom links

List of Classes

Classes of the current edition (2022) are listed in chronological order at the beginning of the table. Classes of previous editions can be found at the end of the table.

ord ID Topic Lecture
I
Lecture
II
Instructors
18 21.1 PLUMED syntax and analysis January 18, 2021 January 25, 2021 M. Bonomi
19 21.2 Statistical errors in MD February 1, 2021 February 8, 2021 G. Tribello
20 21.3 Umbrella sampling February 15, 2021 February 22, 2021 G. Bussi
21 21.4 Metadynamics March 1, 2021 March 8, 2021 M. Bonomi
22 21.5 Replica exchange methods March 15, 2021 March 22, 2021 G. Bussi
23 21.6 Dimensionality reduction April 12, 2021 April 19, 2021 G. Tribello
24 21.7 Optimizing PLUMED performances April 26, 2021 May 3, 2021 M. Bonomi
25 21.8 Poster session May 10, 2021
10 22.00 Introduction to Masterclass 22 (posted on YouTube) January 17, 2022 M. Bonomi
G. Bussi
11 22.01 Funnel-Metadynamics (FM): predicting ligand binding modes, binding free energies and kinetics January 31, 2022 February 7, 2022 V. Limongelli
S. Raniolo
12 22.02 Analysis of Plumed output by Metadynminer February 14, 2022 February 21, 2022 V. Spiwok
13 22.03 Rethinking Metadynamics: the On-the-fly Probability Enhanced Sampling (OPES) method February 28, 2022 March 7, 2022 M. Invernizzi
15 22.05 Machine learning collective variables with Pytorch March 28, 2022 April 4, 2022 L. Bonati
16 22.06 EDS module + Coarse-Grained directed simulations April 26, 2022 May 2, 2022 G. Hocky
A. White
17 22.07 Learning and enhancing fluctuations along information bottleneck for automated enhanced sampling May 9, 2022 May 16, 2022 P. Tiwary
1 22.08 Modelling Concentration-Driven processes with PLUMED May 23, 2022 June 1, 2022 M. Salvalaglio
2 22.09 Using path collective variables to find reaction mechanisms in complex free energy landscapes June 6, 2022 June 13, 2022 B. Ensing
3 22.10 Hamiltonian replica exchange with PLUMED and GROMACS June 21, 2022 June 27, 2022 G. Bussi
4 22.11 Variationally Enhanced Sampling (VES) Module July 4, 2022 July 11, 2022 O. Valsson
5 22.12 Free energy calculations in crystalline solids (EnvironmentSimilarity CV) July 18, 2022 July 25, 2022 P. Piaggi
6 22.13 SASA module - The solvent accessible surface area of proteins as a collective variable, and the application of PLUMED for implicit solvent simulations September 19, 2022 September 26, 2022 A. Arsiccio
8 22.15 Mechanical pulling + FISST module October 17, 2022 October 24, 2022 G. Hocky
G. Stirneman
9.5 22.17 A Bayesian approach to integrate cryo-EM data into MD simulations with PLUMED November 28, 2022 December 5, 2022 M. Bonomi
S. Hoff

By clicking on the Topic of each class, you will be redirected to the material used in the corresponding class. By clicking on Lecture I or Lecture II, you will be redirected to the live recording of the lecture on YouTube.

Practical info

All lectures will take place at 3PM London / 4PM Paris time. The first lecture of each class will last approximately 1 hour, whereas the correction should last about 2 hours. The classes of the second series will be delivered by PLUMED contributors. An introduction to the second series by Max Bonomi and Giovanni Bussi will be posted on YouTube on January 17.

Poster session

At the end of each series of lectures, all participants will be invited to a virtual poster session.

Live vs recorded classes

All lectures will be recorded and promptly made available for those who could not attend the live classes. Participants to the live lectures will have the advantage of:

Resources

Participants are expected to run the exercises using their computing resources. For most of the classes, a laptop with Linux or MacOS will be sufficient. However, for some classes access to a reasonable workstation will be required. The required software will be provided on a conda channel. At this page you can find instructions explaining how to install the basic software needed for most masterclasses.

Participation

For the 2022 series, we do not plan any sign-up procedure. All participants that are online when Lecture I starts will be admitted to the Zoom meeting. They will then receive the invitation for the Slack channel and for Lecture II. Masterclasses are independent of each other, so that you will be able to pick those that you are interested in. The Slack workspace contains a separate private channel for each masterclass (e.g. masterclass-22-1 will be the channel hosting the first masterclass of the 2022 series). If this is not your first masterclass, your user will be added to the relevant channel and you will be notified directly on Slack. More technical information will be made available later.