Browse the lessons

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.

ID Name Instructors Description Tags Actions Modules
25.003 Defining custom machine learning CV with metatomic Guillaume Fraux, Rohit Goswami and Michele Ceriotti An introduction to the use of interface between plumed and the metatomic library   SELECT_COMPONENTS METATOMIC METAD metatomic bias valtools
24.016 Host-Guest binding free energies using an automated OneOPES protocol Pedro Febrer Martinez, Valerio Rizzi, Simone Aureli, Francesco Luigi Gervasio A tutorial on an automated OneOPES protocol for calculating host-guest binding free energies OneOPES, ligand binding, binding free energy, SAMPL challenge, host-guest LOWER_WALLS ECV_MULTITHERMAL FIXEDATOM DISTANCE ENERGY MATHEVAL ANGLE OPES_METAD_EXPLORE OPES_EXPANDED CENTER FIT_TO_TEMPLATE COORDINATION PRINT GROUP WHOLEMOLECULES UPPER_WALLS generic bias function core colvar vatom opes
24.015 How to use the PLUMED PyCV plugin Daniele Rapetti, Toni Giorgino An introduction to the pycv module. This module provides you with an action that allows you to call python from PLUMED. manual, python LOAD DISTANCE PRINT generic colvar setup
24.011 Parameterization of Path CVs for drug-target binding Mattia Bernetti and Matteo Masetti Using path CVs to study drug target binding with metadynamics drug-target binding, Path CVs, metadynamics LOWER_WALLS DISTANCE PATHMSD CENTER MOVINGRESTRAINT PRINT MOLINFO WHOLEMOLECULES METAD UPPER_WALLS generic colvar vatom bias
24.004 Volume-based Metadynamics Riccardo Capelli This tutorial teaches you how to run free energy calculations to investigate protein-ligand binding Metadynamics, protein-ligand binding, free energy calculations HISTOGRAM RESTRAINT POSITION CONVERT_TO_FES FIT_TO_TEMPLATE DUMPGRID WRAPAROUND PRINT GROUP METAD MATHEVAL COM FLUSH RMSD COORDINATION UPPER_WALLS REWEIGHT_BIAS WHOLEMOLECULES READ generic bias function gridtools core colvar vatom
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. masterclass-2022 SECONDARY_STRUCTURE_DRMSD PARABETARMSD ANTIBETARMSD CUSTOM BIASVALUE DISTANCE ALPHARMSD SUM LESS_THAN GYRATION SASA_HASEL PRINT MOLINFO LOWEST generic bias secondarystructure sasa function colvar
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 masterclass-2022 LOWER_WALLS DISTANCE PRINT UNITS METAD UPPER_WALLS generic colvar bias setup
22.002 Analysis of PLUMED output by Metadynminer Vojtech Spiwok An introduction to the R package Metadynminer which can be used to analyse the output from metadynamics simulations masterclass-2022    
22.001 Funnel Metadynamics Stefano Raniolo and Vittorio Limongelli An introduction to modelling ligand binding using funnel metadynamics masterclass-2022 Funnel Metadynamics ligand/target binding    
21.006 Dimensionality reduction Gareth Tribello An introduction to techniques such as dimensionality reduction, path collective variables, and indistinguishability that you may need to use in your own research projects. masterclass-2021 HISTOGRAM DUMPPDB DUMPVECTOR TORSION DUMPGRID UNITS DUMPMULTICOLVAR MORE_THAN SKETCHMAP PATH PRINT FCCUBIC GROUP COMMITTOR CLASSICAL_MDS PARABETARMSD ANTIBETARMSD PCA ALPHARMSD MOLINFO COLLECT_FRAMES LANDMARK_SELECT_FPS RMSD PROJECT_POINTS COORDINATIONNUMBER PCAVARS generic core secondarystructure landmarks setup mapping function gridtools multicolvar symfunc colvar dimred
24.009 Multiple Walkers Metadynamics Simulations with a Reactive Machine Learning Interatomic Potential Kam-Tung Chan and Davide Donadio Running metadynamics with a reactive, machine-learning interaction potential metadynamics, nitrate anion, machine learning interatomic potential CUSTOM UNITS HBOND_MATRIX HISTOGRAM COORDINATION DUMPGRID ANGLE METAD UPPER_WALLS PRINT FLUSH REWEIGHT_METAD READ DISTANCE GROUP colvar setup function bias gridtools adjmat core generic
23.001 Developments in PLUMED Gareth Tribello A series of articles were I outline some development work that I have been doing with PLUMED over the last few years   CLUSTER_WEIGHTS GEOMETRIC_PATH COMBINE LOCAL_AVERAGE COM INTERPOLATE_GRID LOWEST CENTER RMSD_VECTOR SPHERICAL_HARMONIC LOCAL_Q1 DFSCLUSTERING GSYMFUNC_THREEBODY REFERENCE_GRID DISTANCES Q4 GROUP CONCATENATE INTEGRATE_GRID PATH RDF GATHER_REPLICAS PCAVARS INSPHERE CONSTANT MATRIX_VECTOR_PRODUCT FIXEDATOM BIASVALUE TORSION LESS_THAN Q6 ONES GPATH WHOLEMOLECULES SUM DISTANCE PRINT RMSD RESTRAINT KDE CLUSTER_PROPERTIES PAIRENTROPY DOMAIN_DECOMPOSITION DIAGONALIZE CONTACT_MATRIX COORDINATIONNUMBER DUMPGRID MATRIX_PRODUCT TRANSPOSE VOLUME DISPLACEMENT Q1 SORT DISTANCE_MATRIX CUSTOM PDB2CONSTANT ACCUMULATE MORE_THAN SELECT_COMPONENTS HISTOGRAM VSTACK OUTER_PRODUCT GET_VOLUME_ELEMENT DIFFERENCE EUCLIDEAN_DISTANCE POSITION MEAN AVERAGE SPRINT multicolvar matrixtools colvar vatom sprint refdist clusters symfunc mapping function volumes valtools bias gridtools core generic adjmat
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. masterclass-2022    
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. masterclass-2022 MOLINFO EDS MATHEVAL TORSION BIASVALUE DISTANCE PRINT colvar eds bias function generic
25.002 Refining AlphaFold models for virtual screening Samiran Sen A tutorial to use bAIes to refine AlphaFold models for small-molecule virtual screening   BAIES GROUP PRINT BIASVALUE core bias generic isdb
24.021 Setting Up and Analyzing Bias-Exchange Metadynamics Simulations Fabrizio Marinelli and Vanessa Ariadna Leone Alvarez 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. molecular dynamics, metadynamics, bias exchange metadynamics, weighted histogram analysis method, mean forces, cis-trans isomerization, peptidyl-prolyl peptide METAD PRINT RANDOM_EXCHANGES DUMPFORCES TORSION INCLUDE colvar bias generic
24.017 Enhanced sampling for magnesium-RNA binding dynamics Olivier Languin Cattoen This tutorial will teach you how to use PLUMED, GROMACS and Python notebooks to implement an enhanced sampling strategy for magnesium-RNA binding dynamics. CASP, RNA, Magnesium DISTANCES METAD PRINT GROUP CUSTOM BIASVALUE COORDINATION LOWER_WALLS UPPER_WALLS colvar multicolvar function bias generic core
24.013 Permutationally Invariant Networks for Enhanced Sampling (PINES) Nicholas S.M. Herringer, Aniruddha Seal, Armin Shayesteh Zadeh, Siva Dasetty, Andrew L. Ferguson An introduction to using permutationally invariant networks for enhanced sampling Metadynamics, Permutationally invariant vectors, machine learning collective variable, parallel bias metadynamics    
24.008 Using the maze module Jakub Rydzewski Sampling ligand-protein dissociation using the maze module protein, ligand, dissociation, unbinding, maze GROUP CENTER COMMITTOR DISTANCE colvar generic vatom core
24.006 Standard binding free energies from cylindrical restraints Blake I Armstrong, Paolo Raiteri and Julian D Gale Calculating standard binding free energies with metadynamics, PLUMED and OpenMM metadynamics, surface binding, cylindrical restraint, standard state, volume correction, multiple-walkers UNITS RESTART UPPER_WALLS DISTANCE METAD PRINT CUSTOM FLUSH BIASVALUE LOWER_WALLS FIXEDATOM setup colvar function bias generic vatom
24.005 Path integral metadynamics Guillaume Fraux and Michele Ceriotti Incorporating nuclear quantum effects in metadynamics simulations using path integrals Metadynamics, path integrals, nuclear quantum effects DISTANCES DISTANCE METAD SUM PRINT FLUSH LESS_THAN UPPER_WALLS COMBINE colvar function bias generic multicolvar
24.003 Benchmarking PLUMED Daniele Rapetti This tutorial shows you how to use the plumed benchmark tool to measure the performance of the code developers, benchmark, manual PRINT FLUSH COORDINATION colvar generic
24.002 Trans-Cis isomerization in the ground and excited states using PLUMED Adriana Pietropaolo A guide to perform ground and excited state simulations using PLUMED to simulate a trans to cis isomerization process.   WHOLEMOLECULES MATHEVAL CONSTANT PRINT PBMETAD BIASVALUE TORSION colvar bias generic function
24.001 hybrid Small Angle Scattering — hands-on guide Federico Ballabio Practical guide to the use of the hySAS module.   RESTRAINT PRINT STATS GYRATION BIASVALUE ENSEMBLE SAXS MOLINFO colvar function bias generic isdb
23.003 Profiling, GPUs and PLUMED Ketan Bhardwaj A report based on some profiling work on PLUMED that has been performed by the SSEC developers, C++, profiling    
23.002 Introduction to the PLUMED parallel features for developers Daniele Rapetti A simple presentation of some of the available features in PLUMED to simplify the interface with OpenMP and MPI. The lesson contains also a very simple example of how to implement a CV with CUDA. developers, C++, parallelism    
22.011 Variationally Enhanced Sampling Omar Valsson An introduction to running Variationally Enhanced Sampling (VES) using PLUMED. masterclass-2022 Variationally Enhanced Sampling VES HISTOGRAM CONVERT_TO_FES TD_UNIFORM TD_WELLTEMPERED DISTANCE READ PRINT VES_LINEAR_EXPANSION COORDINATION BF_WAVELETS BF_LEGENDRE UPPER_WALLS DUMPGRID OPT_AVERAGED_SGD REWEIGHT_BIAS colvar ves bias generic gridtools
22.003 Rethinking Metadynamics using the OPES method Michele Invernizzi An introduction to the On-the-fly Probability Enhanced Sampling method masterclass-2022 OPES_METAD OPES_EXPANDED ECV_UMBRELLAS_LINE ENERGY ECV_MULTITHERMAL OPES_METAD_EXPLORE TORSION opes colvar
21.003 Umbrella Sampling Giovanni Bussi How to calculate statistical averages and free energy surfaces using umbrella sampling masterclass-2021 CONVERT_TO_FES READ RESTRAINT PRINT CUSTOM BIASVALUE MOLINFO DUMPGRID TORSION HISTOGRAM REWEIGHT_BIAS colvar function bias generic gridtools
21.002 Statistical errors in MD Gareth Tribello How to calculate errors on averages calculated from unbiased and biased MD simulations using the method of block averages. masterclass-2021 UNITS CONVERT_TO_FES UPPER_WALLS READ RESTRAINT PRINT CONSTANT CUSTOM DISTANCE COM COORDINATIONNUMBER METAD AVERAGE DUMPGRID HISTOGRAM REWEIGHT_BIAS setup colvar function bias generic vatom symfunc gridtools
26.001 Mastering Enhanced Sampling with OneOPES Valerio Rizzi 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   DISTANCE TORSION MOLINFO PRINT ENERGY ENDPLUMED OPES_EXPANDED OPES_METAD_EXPLORE ECV_MULTITHERMAL colvar opes generic
25.004 An introduction to statistical mechanics for undergraduate students Gareth Tribello These are the resources that I provide to students at Queen’s Unviersity Belfast for the third year course in statistical mechanics      
25.001 VisMetaDynamics Christian Phillips 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      
24.020 An introduction to CpH-Metadynamics simulations Tomas Silva This tutorial aims to train users to perform CpH-Metadynamics simulations using the stochastic titration constant-pH Molecular Dynamics method and PLUMED. RNA, Constant pH    
24.019 ASE-PLUMED interface Daniel Sucerquia, Pilar Cossio, Olga Lopez-Acevedo Using PLUMED from ASE atomistic calculations, ab-initio, molecular dynamics UNITS METAD COMBINE COORDINATIONNUMBER CUSTOM ONES FLUSH PRINT UPPER_WALLS GYRATION MATRIX_VECTOR_PRODUCT LOWER_WALLS GROUP MEAN CONTACT_MATRIX DISTANCE COORDINATION COM bias matrixtools core symfunc colvar setup function adjmat generic vatom
24.018 Permutation Invariant Vector and Water Crystallisation Silvio Pipolo, Fabio Pietrucci Modelling water crystallisation using PIV variables PIV, PathCV, Water Crystallisation METAD FUNCPATHMSD PIV UPPER_WALLS PRINT LOWER_WALLS CELL bias colvar piv function generic
24.014 Alpha-Fold Metainference for structural ensemble prediction of a partially disordered protein Faidon Brotzakis, Hussein Murtada and Michele Vendruscolo A tutorial about how metainference can be used in tandem with Alpha-fold to predict the ensemble of structures for a partially disordered protein. Protein dynamics, AlphaFold2, Metainference, PB-MetaD, CALVADOS2, partially disordered proteins RMSD TORSION MOLINFO WHOLEMOLECULES UPPER_WALLS GYRATION PRINT METAINFERENCE FLUSH CONSTANT ENDPLUMED CONTACTMAP CENTER PBMETAD bias colvar isdb generic vatom
24.012 Exploring Free Energy Surfaces with MACE-PLUMED Metadynamics S.G.H. Brookes, C. Schran, A. Michaelides Performing metadynamics simulations with LAMMPS, MACE and PLUMED metadynamics, machine learning UNITS PRINT generic setup
24.010 Modelling mechanobiological processes Claire Pritchard, Guillaume Stirnemann and Glen Hocky A tutorial on modelling mechanobiological processes Metadynamics, pulling, force, rates, GPCR UNITS COMMITTOR METAD RESTRAINT BIASVALUE MATHEVAL PRINT DISTANCE DUMPATOMS COM bias colvar setup function generic vatom
24.007 Transition-Tempered Metadynamics Jiangbo Wu and Gregory A. Voth An introduction to the transition tempered metadynamics method metadynamics, free energy sampling, reaction mechanism UNITS METAD RESTART RESTRAINT EXTENDED_LAGRANGIAN TORSION MOLINFO WHOLEMOLECULES PRINT UPPER_WALLS FLUSH LOWER_WALLS GROUP DISTANCE COORDINATION COM bias core colvar setup generic vatom
23.004 Rewriting coordination CVs in CUDA Daniele Rapetti How to implement a basic version of the coordination CV with CUDA developers, C++, parallelism, Cuda    
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. masterclass-2022 BIASVALUE MOLINFO EMMIVOX WHOLEMOLECULES PRINT GROUP core isdb generic bias
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 masterclass-2022 UNITS METAD RESTRAINT BIASVALUE MATHEVAL PRINT FISST DISTANCE DUMPATOMS bias colvar fisst setup function generic
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 masterclass-2022 HISTOGRAM CUSTOM MATHEVAL ONES UPPER_WALLS OPES_METAD ENVIRONMENTSIMILARITY DISTANCE_MATRIX GROUP MATRIX_VECTOR_PRODUCT SUM MEAN Q6 LOWER_WALLS MORE_THAN DUMPGRID bias matrixtools core symfunc opes function gridtools envsim adjmat generic
22.010 Hamiltonian replica exchange with PLUMED and GROMACS Giovanni Bussi An introduction to running Hamiltonian replica exchange calculations using PLUMED and GROMACS. masterclass-2022 TORSION MOLINFO PRINT colvar generic
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. masterclass-2022 RESTRAINT CLUSTER_DISTRIBUTION COORDINATIONNUMBER ONES FLUSH PRINT MATRIX_VECTOR_PRODUCT GROUP SUM CONTACT_MATRIX DFSCLUSTERING CLUSTER_NATOMS MORE_THAN bias matrixtools core symfunc clusters function adjmat generic
22.005 Machine learning collective variables with PyTorch Luigi Bonati An introduction to designing data-driven CVs using two methods (DeepLDA and DeepTICA). masterclass-2022 TORSION PYTORCH_MODEL PRINT colvar generic pytorch
21.007 Optimizing PLUMED performances Max Bonomi Some lessons on monitoring and improving the performance of PLUMED and gromacs masterclass-2021 EFFECTIVE_ENERGY_DRIFT METAD COMBINE RMSD CUSTOM WHOLEMOLECULES PRINT DEBUG GROUP DISTANCE COORDINATION bias core colvar function generic
21.005 Replica exchange methods Giovanni Bussi Running umbrella sampling with replica exchange, bias exchange metadynamics and parallel tempering metadynamics masterclass-2021 METAD RESTRAINT TORSION MOLINFO RANDOM_EXCHANGES PRINT colvar generic bias
21.004 Metadynamics Max Bonomi How to calculate statistical averages and free energy surfaces using metadynamics masterclass-2021 METAD REWEIGHT_BIAS HISTOGRAM TORSION MOLINFO PRINT CONVERT_TO_FES DUMPGRID colvar generic bias gridtools
21.001 PLUMED syntax and analysis Max Bonomi Basic features of the PLUMED input syntax with a particular focus on PBCs and selection tools masterclass-2021 ALPHARMSD COMBINE TORSION MOLINFO WHOLEMOLECULES PRINT GYRATION PARABETARMSD ANTIBETARMSD CENTER DISTANCE DUMPATOMS secondarystructure colvar function generic vatom
20.001 Installing PLUMED Gareth Tribello An interactive tutorial resource on compiling PLUMED and linking it with MD codes.