PLUMED-TUTORIALS

Browse the lessons

The graph below shows a subset of the lessons that have been submitted to the PLUMED-TUTORIALS website and suggests an order for working through them. PLUMED-TUTORIAL 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 .

You can return to a complete list of the tutorials by clicking here.

%%{init: {"flowchart": {"defaultRenderer": "elk"}} }%%
   
flowchart TD
0("Multiple Walkers Metadynamics
Simulations with a Reactive
Machine Learning Interatomic
Potential")
1("PLUMED syntax and analysis")
2("Statistical errors in MD")
3("Metadynamics")
4("EDS module and Coarse-Grained
directed simulations")
5("Mastering Enhanced Sampling
with OneOPES")
6("Replica exchange methods")
7("Rethinking Metadynamics using
the OPES method")
8("Host-Guest binding free
energies using an automated
OneOPES protocol")
9("VisMetaDynamics")
10("An introduction to CpH-
Metadynamics simulations")
11("ASE-PLUMED interface")
12("Alpha-Fold Metainference for
structural ensemble prediction
of a partially disordered
protein")
13("Exploring Free Energy Surfaces
with MACE-PLUMED Metadynamics")
14("Modelling mechanobiological
processes")
15("Mechanical pulling + FISST
module")
16("Transition-Tempered
Metadynamics")
17("A Bayesian approach to
integrate cryo-EM data into MD
simulations with PLUMED")
18("Free energy calculations in
crystalline solids")
19("Hamiltonian replica exchange
with PLUMED and GROMACS")
20("Modelling Concentration-driven
processes with PLUMED")
21("Machine learning collective
variables with PyTorch")
22("Optimizing PLUMED performances")
23("Umbrella Sampling")
24("Installing PLUMED")
25("Defining custom machine
learning CV with metatomic")
26("Parameterization of Path CVs
for drug-target binding")
27("Volume-based Metadynamics")
28("SASA module - The solvent
accessible surface area of
proteins as a collective
variable, and the application
of PLUMED for implicit solvent
simulations")
29("Using path collective
variables to find reaction
mechanisms in complex free
energy landscapes")
30("Analysis of PLUMED output by
Metadynminer")
31("Dimensionality reduction")
32("Refining AlphaFold models for
virtual screening")
33("Setting Up and Analyzing Bias-
Exchange Metadynamics
Simulations")
34("Enhanced sampling for
magnesium-RNA binding dynamics")
35("Permutationally Invariant
Networks for Enhanced Sampling
(PINES)")
36("Using the maze module")
37("Standard binding free energies
from cylindrical restraints")
38("Path integral metadynamics")
subgraph g0 [ ]
0("Multiple Walkers Metadynamics
Simulations with a Reactive
Machine Learning Interatomic
Potential")
34("Enhanced sampling for
magnesium-RNA binding dynamics")
35("Permutationally Invariant
Networks for Enhanced Sampling
(PINES)")
37("Standard binding free energies
from cylindrical restraints")
6("Replica exchange methods")
7("Rethinking Metadynamics using
the OPES method")
0~~~7;
38("Path integral metadynamics")
34~~~38;
9("VisMetaDynamics")
35~~~9;
10("An introduction to CpH-
Metadynamics simulations")
37~~~10;
13("Exploring Free Energy Surfaces
with MACE-PLUMED Metadynamics")
6~~~13;
16("Transition-Tempered
Metadynamics")
7~~~16;
25("Defining custom machine
learning CV with metatomic")
38~~~25;
26("Parameterization of Path CVs
for drug-target binding")
9~~~26;
27("Volume-based Metadynamics")
10~~~27;
28("SASA module - The solvent
accessible surface area of
proteins as a collective
variable, and the application
of PLUMED for implicit solvent
simulations")
13~~~28;
30("Analysis of PLUMED output by
Metadynminer")
16~~~30;
end
3("Metadynamics")
3--> g0;
subgraph g2 [ ]
32("Refining AlphaFold models for
virtual screening")
33("Setting Up and Analyzing Bias-
Exchange Metadynamics
Simulations")
2("Statistical errors in MD")
4("EDS module and Coarse-Grained
directed simulations")
36("Using the maze module")
11("ASE-PLUMED interface")
32~~~11;
12("Alpha-Fold Metainference for
structural ensemble prediction
of a partially disordered
protein")
33~~~12;
15("Mechanical pulling + FISST
module")
2~~~15;
17("A Bayesian approach to
integrate cryo-EM data into MD
simulations with PLUMED")
4~~~17;
20("Modelling Concentration-driven
processes with PLUMED")
36~~~20;
29("Using path collective
variables to find reaction
mechanisms in complex free
energy landscapes")
11~~~29;
31("Dimensionality reduction")
12~~~31;
end
1("PLUMED syntax and analysis")
1--> g2;
2-->23;
5("Mastering Enhanced Sampling
with OneOPES")
6-->5;
6-->19;
6-->22;
7-->5;
7-->18;
7-->21;
8("Host-Guest binding free
energies using an automated
OneOPES protocol")
8-->5;
14("Modelling mechanobiological
processes")
15-->14;
18("Free energy calculations in
crystalline solids")
19("Hamiltonian replica exchange
with PLUMED and GROMACS")
21("Machine learning collective
variables with PyTorch")
22("Optimizing PLUMED performances")
23("Umbrella Sampling")
23-->3;
24("Installing PLUMED")
24-->1;
click 0 "lessons/24/009/data/NAVIGATION.html" "Running metadynamics with a reactive, machine-learning interaction potential [Authors: Kam-Tung Chan and Davide Donadio]"
click 1 "lessons/21/001/data/NAVIGATION.html" "Basic features of the PLUMED input syntax with a particular focus on PBCs and selection tools [Authors: Max Bonomi]"
click 2 "lessons/21/002/data/NAVIGATION.html" "How to calculate errors on averages calculated from unbiased and biased MD simulations using the method of block averages. [Authors: Gareth Tribello]"
click 3 "lessons/21/004/data/NAVIGATION.html" "How to calculate statistical averages and free energy surfaces using metadynamics [Authors: Max Bonomi]"
click 4 "lessons/22/006/data/NAVIGATION.html" "This tutorials describes how to bias simulations to agree with experimental data using experiment directed simulation. [Authors: Glen Hocky and Andrew White]"
click 5 "lessons/26/001/data/NAVIGATION.html" "A tutorial on sampling with OneOPES that was prepared for the Next-Generation Molecular Modelling Summer School that was held in Pula, Italy from July 27th to 31st 2026 [Authors: Valerio Rizzi]"
click 6 "lessons/21/005/data/NAVIGATION.html" "Running umbrella sampling with replica exchange, bias exchange metadynamics and parallel tempering metadynamics [Authors: Giovanni Bussi]"
click 7 "lessons/22/003/data/NAVIGATION.html" "An introduction to the On-the-fly Probability Enhanced Sampling method [Authors: Michele Invernizzi]"
click 8 "lessons/24/016/data/NAVIGATION.html" "A tutorial on an automated OneOPES protocol for calculating host-guest binding free energies [Authors: Pedro Febrer Martinez, Valerio Rizzi, Simone Aureli, Francesco Luigi Gervasio]"
click 9 "lessons/25/001/data/NAVIGATION.html" "A graphical tool that allows you to visually inspect how the free energy surface for a metadynamics simulation is affected by the choice of hyperparameters [Authors: Christian Phillips]"
click 10 "lessons/24/020/data/NAVIGATION.html" "This tutorial aims to train users to perform CpH-Metadynamics simulations using the stochastic titration constant-pH Molecular Dynamics method and PLUMED. [Authors: Tomas Silva]"
click 11 "lessons/24/019/data/NAVIGATION.html" "Using PLUMED from ASE [Authors: Daniel Sucerquia, Pilar Cossio, Olga Lopez-Acevedo]"
click 12 "lessons/24/014/data/NAVIGATION.html" "A tutorial about how metainference can be used in tandem with Alpha-fold to predict the ensemble of structures for a partially disordered protein. [Authors: Faidon Brotzakis, Hussein Murtada and Michele Vendruscolo]"
click 13 "lessons/24/012/data/NAVIGATION.html" "Performing metadynamics simulations with LAMMPS, MACE and PLUMED [Authors: S.G.H. Brookes, C. Schran, A. Michaelides]"
click 14 "lessons/24/010/data/NAVIGATION.html" "A tutorial on modelling mechanobiological processes [Authors: Claire Pritchard, Guillaume Stirnemann and Glen Hocky]"
click 15 "lessons/22/015/data/NAVIGATION.html" "This tutorial explains how mechanical forces can be modeled using PLUMED and the FISST module [Authors: Guillaume Stirnemann and Glen Hocky]"
click 16 "lessons/24/007/data/NAVIGATION.html" "An introduction to the transition tempered metadynamics method [Authors: Jiangbo Wu and Gregory A. Voth]"
click 17 "lessons/22/017/data/NAVIGATION.html" "How to use PLUMED to perform single-structure and ensemble refinement using cryo-EM maps and EMMIVox. [Authors: Samuel Hoff and Max Bonomi]"
click 18 "lessons/22/012/data/NAVIGATION.html" "An introduction to the Environmental similarity CV and the calculation of chemical potentials of liquids and solids [Authors: Pablo Piaggi]"
click 19 "lessons/22/010/data/NAVIGATION.html" "An introduction to running Hamiltonian replica exchange calculations using PLUMED and GROMACS. [Authors: Giovanni Bussi]"
click 20 "lessons/22/008/data/NAVIGATION.html" "An introduction to the tools that are available in PLUMED for simulating concentration-driven processes such as nucleation, growth and diffusion. [Authors: Matteo Salvalaglio]"
click 21 "lessons/22/005/data/NAVIGATION.html" "An introduction to designing data-driven CVs using two methods (DeepLDA and DeepTICA). [Authors: Luigi Bonati]"
click 22 "lessons/21/007/data/NAVIGATION.html" "Some lessons on monitoring and improving the performance of PLUMED and gromacs [Authors: Max Bonomi]"
click 23 "lessons/21/003/data/NAVIGATION.html" "How to calculate statistical averages and free energy surfaces using umbrella sampling [Authors: Giovanni Bussi]"
click 24 "lessons/20/001/data/NAVIGATION.html" "An interactive tutorial resource on compiling PLUMED and linking it with MD codes. [Authors: Gareth Tribello]"
click 25 "lessons/25/003/data/NAVIGATION.html" "An introduction to the use of interface between plumed and the metatomic library [Authors: Guillaume Fraux, Rohit Goswami and Michele Ceriotti]"
click 26 "lessons/24/011/data/NAVIGATION.html" "Using path CVs to study drug target binding with metadynamics [Authors: Mattia Bernetti and Matteo Masetti]"
click 27 "lessons/24/004/data/NAVIGATION.html" "This tutorial teaches you how to run free energy calculations to investigate protein-ligand binding [Authors: Riccardo Capelli]"
click 28 "lessons/22/013/data/NAVIGATION.html" "An introduction to the SASA module and a description of how PLUMED can be used for implicit solvent simulations. [Authors: Andrea Arsiccio]"
click 29 "lessons/22/009/data/NAVIGATION.html" "An introduction to using path collective variables for describing and simulating activated molecular processes [Authors: Bernd Ensing]"
click 30 "lessons/22/002/data/NAVIGATION.html" "An introduction to the R package Metadynminer which can be used to analyse the output from metadynamics simulations [Authors: Vojtech Spiwok]"
click 31 "lessons/21/006/data/NAVIGATION.html" "An introduction to techniques such as dimensionality reduction, path collective variables, and indistinguishability that you may need to use in your own research projects. [Authors: Gareth Tribello]"
click 32 "lessons/25/002/data/NAVIGATION.html" "A tutorial to use bAIes to refine AlphaFold models for small-molecule virtual screening [Authors: Samiran Sen]"
click 33 "lessons/24/021/data/NAVIGATION.html" "This tutorial offers a comprehensive protocol, complemented by practical examples, for setting up and performing free energy analysis of bias-exchange metadynamics simulations of cis-trans isomerization in a proline-containing peptide. [Authors: Fabrizio Marinelli and Vanessa Ariadna Leone Alvarez]"
click 34 "lessons/24/017/data/NAVIGATION.html" "This tutorial will teach you how to use PLUMED, GROMACS and Python notebooks to implement an enhanced sampling strategy for magnesium-RNA binding dynamics. [Authors: Olivier Languin Cattoen]"
click 35 "lessons/24/013/data/NAVIGATION.html" "An introduction to using permutationally invariant networks for enhanced sampling [Authors: Nicholas S.M. Herringer, Aniruddha Seal, Armin Shayesteh Zadeh, Siva Dasetty, Andrew L. Ferguson]"
click 36 "lessons/24/008/data/NAVIGATION.html" "Sampling ligand-protein dissociation using the maze module [Authors: Jakub Rydzewski]"
click 37 "lessons/24/006/data/NAVIGATION.html" "Calculating standard binding free energies with metadynamics, PLUMED and OpenMM [Authors: Blake I Armstrong, Paolo Raiteri and Julian D Gale]"
click 38 "lessons/24/005/data/NAVIGATION.html" "Incorporating nuclear quantum effects in metadynamics simulations using path integrals [Authors: Guillaume Fraux and Michele Ceriotti]"