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The lessons that have been submitted to the PLUMED-TUTORIALS are listed below. PLUMED-TUTORIALS monitors whether PLUMED input files in these lessons are compatible with the current and development versions of the code and integrates links from these files to the PLUMED manual. Inputs in the tutorials listed below were last tested on .

Suggestions for an order to work through the tutorials can be found here. A complete bibliography of papers connected to these lessons can be found here.

Showing 1 to 10 of 14 entries (filtered from 48 total entries)

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ID	Name	Instructors	Description
22.017	A Bayesian approach to integrate cryo-EM data into MD simulations with PLUMED	Samuel Hoff and Max Bonomi	How to use PLUMED to perform single-structure and ensemble refinement using cryo-EM maps and EMMIVox.
22.015	Mechanical pulling + FISST module	Guillaume Stirnemann and Glen Hocky	This tutorial explains how mechanical forces can be modeled using PLUMED and the FISST module
22.013	SASA module - The solvent accessible surface area of proteins as a collective variable, and the application of PLUMED for implicit solvent simulations	Andrea Arsiccio	An introduction to the SASA module and a description of how PLUMED can be used for implicit solvent simulations.
22.012	Free energy calculations in crystalline solids	Pablo Piaggi	An introduction to the Environmental similarity CV and the calculation of chemical potentials of liquids and solids
22.011	Variationally Enhanced Sampling	Omar Valsson	An introduction to running Variationally Enhanced Sampling (VES) using PLUMED.
22.010	Hamiltonian replica exchange with PLUMED and GROMACS	Giovanni Bussi	An introduction to running Hamiltonian replica exchange calculations using PLUMED and GROMACS.
22.009	Using path collective variables to find reaction mechanisms in complex free energy landscapes	Bernd Ensing	An introduction to using path collective variables for describing and simulating activated molecular processes
22.008	Modelling Concentration-driven processes with PLUMED	Matteo Salvalaglio	An introduction to the tools that are available in PLUMED for simulating concentration-driven processes such as nucleation, growth and diffusion.
22.007	Learning and enhancing fluctuations along information bottleneck for automated enhanced sampling	Pratyush Tiwary	An introduction to the state predictive information bottleneck (SPIB) deep-learning-based framework for learning reaction coordinates from high dimensional molecular simulation trajectories.
22.006	EDS module and Coarse-Grained directed simulations	Glen Hocky and Andrew White	This tutorials describes how to bias simulations to agree with experimental data using experiment directed simulation.

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PLUMED-TUTORIALS

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