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("ASE-PLUMED interface")
1("PLUMED syntax and analysis")
2("Permutationally Invariant
Networks for Enhanced Sampling
(PINES)")
3("Metadynamics")
4("Modelling mechanobiological
processes")
5("Mechanical pulling + FISST
module")
6("Volume-based Metadynamics")
7("Free energy calculations in
crystalline solids")
8("Rethinking Metadynamics using
the OPES method")
9("Using path collective
variables to find reaction
mechanisms in complex free
energy landscapes")
10("EDS module and Coarse-Grained
directed simulations")
11("Machine learning collective
variables with PyTorch")
12("Statistical errors in MD")
13("Installing PLUMED")
14("Defining custom machine
learning CV with metatomic")
15("Enhanced sampling for
magnesium-RNA binding dynamics")
16("Hamiltonian replica exchange
with PLUMED and GROMACS")
17("Replica exchange methods")
18("Optimizing PLUMED performances")
19("Umbrella Sampling")
20("VisMetaDynamics")
21("Alpha-Fold Metainference for
structural ensemble prediction
of a partially disordered
protein")
22("Using the maze module")
23("Standard binding free energies
from cylindrical restraints")
24("Modelling Concentration-driven
processes with PLUMED")
25("Analysis of PLUMED output by
Metadynminer")
26("Dimensionality reduction")
27("Refining AlphaFold models for
virtual screening")
28("Setting Up and Analyzing Bias-
Exchange Metadynamics
Simulations")
29("An introduction to CpH-
Metadynamics simulations")
30("Exploring Free Energy Surfaces
with MACE-PLUMED Metadynamics")
31("Parameterization of Path CVs
for drug-target binding")
32("Multiple Walkers Metadynamics
Simulations with a Reactive
Machine Learning Interatomic
Potential")
33("Transition-Tempered
Metadynamics")
34("Path integral metadynamics")
35("A Bayesian approach to
integrate cryo-EM data into MD
simulations with PLUMED")
36("SASA module - The solvent
accessible surface area of
proteins as a collective
variable, and the application
of PLUMED for implicit solvent
simulations")
subgraph g0 [ ]
0("ASE-PLUMED interface")
35("A Bayesian approach to
integrate cryo-EM data into MD
simulations with PLUMED")
5("Mechanical pulling + FISST
module")
9("Using path collective
variables to find reaction
mechanisms in complex free
energy landscapes")
10("EDS module and Coarse-Grained
directed simulations")
12("Statistical errors in MD")
0~~~12;
21("Alpha-Fold Metainference for
structural ensemble prediction
of a partially disordered
protein")
35~~~21;
22("Using the maze module")
5~~~22;
24("Modelling Concentration-driven
processes with PLUMED")
9~~~24;
26("Dimensionality reduction")
10~~~26;
27("Refining AlphaFold models for
virtual screening")
12~~~27;
28("Setting Up and Analyzing Bias-
Exchange Metadynamics
Simulations")
21~~~28;
end
1("PLUMED syntax and analysis")
1--> g0;
subgraph g2 [ ]
32("Multiple Walkers Metadynamics
Simulations with a Reactive
Machine Learning Interatomic
Potential")
33("Transition-Tempered
Metadynamics")
2("Permutationally Invariant
Networks for Enhanced Sampling
(PINES)")
34("Path integral metadynamics")
36("SASA module - The solvent
accessible surface area of
proteins as a collective
variable, and the application
of PLUMED for implicit solvent
simulations")
6("Volume-based Metadynamics")
32~~~6;
8("Rethinking Metadynamics using
the OPES method")
33~~~8;
14("Defining custom machine
learning CV with metatomic")
2~~~14;
15("Enhanced sampling for
magnesium-RNA binding dynamics")
34~~~15;
17("Replica exchange methods")
36~~~17;
20("VisMetaDynamics")
6~~~20;
23("Standard binding free energies
from cylindrical restraints")
8~~~23;
25("Analysis of PLUMED output by
Metadynminer")
14~~~25;
29("An introduction to CpH-
Metadynamics simulations")
15~~~29;
30("Exploring Free Energy Surfaces
with MACE-PLUMED Metadynamics")
17~~~30;
31("Parameterization of Path CVs
for drug-target binding")
20~~~31;
end
3("Metadynamics")
3--> g2;
4("Modelling mechanobiological
processes")
5-->4;
7("Free energy calculations in
crystalline solids")
8-->7;
8-->11;
11("Machine learning collective
variables with PyTorch")
12-->19;
13("Installing PLUMED")
13-->1;
16("Hamiltonian replica exchange
with PLUMED and GROMACS")
17-->16;
17-->18;
18("Optimizing PLUMED performances")
19("Umbrella Sampling")
19-->3;
click 0 "lessons/24/019/data/NAVIGATION.html" "Using PLUMED from ASE [Authors: Daniel Sucerquia, Pilar Cossio, Olga Lopez-Acevedo]"
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/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 3 "lessons/21/004/data/NAVIGATION.html" "How to calculate statistical averages and free energy surfaces using metadynamics [Authors: Max Bonomi]"
click 4 "lessons/24/010/data/NAVIGATION.html" "A tutorial on modelling mechanobiological processes [Authors: Claire Pritchard, Guillaume Stirnemann and Glen Hocky]"
click 5 "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 6 "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 7 "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 8 "lessons/22/003/data/NAVIGATION.html" "An introduction to the On-the-fly Probability Enhanced Sampling method [Authors: Michele Invernizzi]"
click 9 "lessons/22/009/data/NAVIGATION.html" "An introduction to using path collective variables for describing and simulating activated molecular processes [Authors: Bernd Ensing]"
click 10 "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 11 "lessons/22/005/data/NAVIGATION.html" "An introduction to designing data-driven CVs using two methods (DeepLDA and DeepTICA). [Authors: Luigi Bonati]"
click 12 "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 13 "lessons/20/001/data/NAVIGATION.html" "An interactive tutorial resource on compiling PLUMED and linking it with MD codes. [Authors: Gareth Tribello]"
click 14 "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 15 "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 16 "lessons/22/010/data/NAVIGATION.html" "An introduction to running Hamiltonian replica exchange calculations using PLUMED and GROMACS. [Authors: Giovanni Bussi]"
click 17 "lessons/21/005/data/NAVIGATION.html" "Running umbrella sampling with replica exchange, bias exchange metadynamics and parallel tempering metadynamics [Authors: Giovanni Bussi]"
click 18 "lessons/21/007/data/NAVIGATION.html" "Some lessons on monitoring and improving the performance of PLUMED and gromacs [Authors: Max Bonomi]"
click 19 "lessons/21/003/data/NAVIGATION.html" "How to calculate statistical averages and free energy surfaces using umbrella sampling [Authors: Giovanni Bussi]"
click 20 "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 21 "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 22 "lessons/24/008/data/NAVIGATION.html" "Sampling ligand-protein dissociation using the maze module [Authors: Jakub Rydzewski]"
click 23 "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 24 "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 25 "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 26 "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 27 "lessons/25/002/data/NAVIGATION.html" "A tutorial to use bAIes to refine AlphaFold models for small-molecule virtual screening [Authors: Samiran Sen]"
click 28 "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 29 "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 30 "lessons/24/012/data/NAVIGATION.html" "Performing metadynamics simulations with LAMMPS, MACE and PLUMED [Authors: S.G.H. Brookes, C. Schran, A. Michaelides]"
click 31 "lessons/24/011/data/NAVIGATION.html" "Using path CVs to study drug target binding with metadynamics [Authors: Mattia Bernetti and Matteo Masetti]"
click 32 "lessons/24/009/data/NAVIGATION.html" "Running metadynamics with a reactive, machine-learning interaction potential [Authors: Kam-Tung Chan and Davide Donadio]"
click 33 "lessons/24/007/data/NAVIGATION.html" "An introduction to the transition tempered metadynamics method [Authors: Jiangbo Wu and Gregory A. Voth]"
click 34 "lessons/24/005/data/NAVIGATION.html" "Incorporating nuclear quantum effects in metadynamics simulations using path integrals [Authors: Guillaume Fraux and Michele Ceriotti]"
click 35 "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 36 "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]"