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
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 FIXEDATOM BIASVALUE FLUSH METAD PRINT DISTANCE LOWER_WALLS UNITS CUSTOM RESTART UPPER_WALLS colvar vatom function setup bias generic
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 KDE CONVERT_TO_FES ONES WRAPAROUND COM RESTRAINT WHOLEMOLECULES DUMPGRID HISTOGRAM UPPER_WALLS READ POSITION REWEIGHT_BIAS MATHEVAL METAD RMSD COORDINATION CUSTOM GROUP FLUSH PRINT FIT_TO_TEMPLATE ACCUMULATE colvar core vatom function gridtools bias generic
22.011 Variationally Enhanced Sampling Omar Valsson An introduction to running Variationally Enhanced Sampling (VES) using PLUMED. masterclass-2022 Variationally Enhanced Sampling VES REWEIGHT_BIAS CONVERT_TO_FES TD_UNIFORM PRINT OPT_AVERAGED_SGD BF_LEGENDRE COORDINATION DISTANCE TD_WELLTEMPERED HISTOGRAM DUMPGRID VES_LINEAR_EXPANSION BF_WAVELETS UPPER_WALLS READ colvar ves gridtools bias 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 PRINT MOLINFO colvar generic
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    
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    
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   OUTER_PRODUCT MEAN RDF EUCLIDEAN_DISTANCE Q6 INSPHERE REFERENCE_GRID INTERPOLATE_GRID HISTOGRAM COMBINE LESS_THAN GPATH SORT SPRINT DISTANCE_MATRIX TORSION COORDINATIONNUMBER LOWEST WHOLEMOLECULES PATH DOMAIN_DECOMPOSITION LOCAL_AVERAGE DFSCLUSTERING ACCUMULATE CLUSTER_PROPERTIES GEOMETRIC_PATH PRINT PDB2CONSTANT ONES SELECT_COMPONENTS Q4 GROUP AVERAGE SUM RESTRAINT MATRIX_VECTOR_PRODUCT CONTACT_MATRIX COM CONCATENATE RMSD INTEGRATE_GRID LOCAL_Q1 SPHERICAL_HARMONIC DUMPGRID GSYMFUNC_THREEBODY MATRIX_PRODUCT VSTACK CONSTANT GATHER_REPLICAS MORE_THAN POSITION DIFFERENCE PAIRENTROPY CENTER VOLUME FIXEDATOM Q1 KDE DISTANCES RMSD_VECTOR TRANSPOSE DISTANCE DIAGONALIZE GET_VOLUME_ELEMENT CUSTOM DISPLACEMENT PCAVARS BIASVALUE CLUSTER_WEIGHTS volumes valtools symfunc multicolvar generic clusters matrixtools refdist adjmat mapping function bias vatom colvar sprint core gridtools
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 PRINT DISTANCE EDS TORSION BIASVALUE MATHEVAL generic bias eds function colvar
21.007 Optimizing PLUMED performances Max Bonomi Some lessons on monitoring and improving the performance of PLUMED and gromacs masterclass-2021 RMSD WHOLEMOLECULES EFFECTIVE_ENERGY_DRIFT METAD COMBINE PRINT DISTANCE DEBUG CUSTOM GROUP COORDINATION generic bias function colvar core
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      
25.003 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   METAD SELECT_COMPONENTS METATOMIC metatomic valtools bias
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 BIASVALUE PRINT isdb core generic bias
24.019 ASE-PLUMED interface Daniel Sucerquia, Pilar Cossio, Olga Lopez-Acevedo Using PLUMED from ASE atomistic calculations, ab-initio, molecular dynamics METAD ONES UNITS MEAN COMBINE COORDINATIONNUMBER COM GYRATION PRINT UPPER_WALLS MATRIX_VECTOR_PRODUCT DISTANCE CONTACT_MATRIX CUSTOM GROUP COORDINATION LOWER_WALLS FLUSH function vatom generic matrixtools adjmat symfunc core setup bias colvar
24.018 Permutation Invariant Vector and Water Crystallisation Silvio Pipolo, Fabio Pietrucci Modelling water crystallisation using PIV variables PIV, PathCV, Water Crystallisation FUNCPATHMSD LOWER_WALLS METAD PIV PRINT UPPER_WALLS CELL function generic piv bias colvar
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 METAD BIASVALUE UPPER_WALLS PRINT CUSTOM GROUP COORDINATION LOWER_WALLS DISTANCES function generic multicolvar core bias colvar
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 ENERGY UPPER_WALLS CENTER ANGLE PRINT FIXEDATOM DISTANCE OPES_EXPANDED ECV_MULTITHERMAL MATHEVAL OPES_METAD_EXPLORE GROUP COORDINATION LOWER_WALLS WHOLEMOLECULES FIT_TO_TEMPLATE opes function vatom generic core bias colvar
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 DISTANCE PRINT LOAD setup generic colvar
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    
24.012 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
24.003 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 FLUSH COORDINATION PRINT 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.   PBMETAD TORSION BIASVALUE PRINT MATHEVAL CONSTANT WHOLEMOLECULES colvar function generic bias
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 MOLINFO LESS_THAN GYRATION BIASVALUE PRINT ANTIBETARMSD DISTANCE SUM CUSTOM SECONDARY_STRUCTURE_DRMSD ALPHARMSD PARABETARMSD LOWEST SASA_HASEL function sasa generic secondarystructure bias colvar
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 DUMPGRID HISTOGRAM ONES MEAN ENVIRONMENTSIMILARITY UPPER_WALLS MATRIX_VECTOR_PRODUCT Q6 OPES_METAD SUM CUSTOM MORE_THAN MATHEVAL DISTANCE_MATRIX GROUP LOWER_WALLS opes function envsim generic gridtools matrixtools adjmat symfunc core bias
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    
22.005 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 generic pytorch colvar
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    
21.005 Replica exchange methods Giovanni Bussi Running umbrella sampling with replica exchange, bias exchange metadynamics and parallel tempering metadynamics masterclass-2021 METAD MOLINFO TORSION RANDOM_EXCHANGES PRINT RESTRAINT colvar generic bias
21.004 Metadynamics Max Bonomi How to calculate statistical averages and free energy surfaces using metadynamics masterclass-2021 DUMPGRID METAD HISTOGRAM MOLINFO CONVERT_TO_FES REWEIGHT_BIAS TORSION PRINT gridtools generic bias colvar
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 DUMPGRID CONVERT_TO_FES HISTOGRAM UNITS METAD REWEIGHT_BIAS COORDINATIONNUMBER COM PRINT UPPER_WALLS DISTANCE READ CUSTOM CONSTANT AVERAGE RESTRAINT function vatom generic gridtools symfunc bias setup colvar
20.001 Installing PLUMED Gareth Tribello An interactive tutorial resource on compiling PLUMED and linking it with MD codes.      
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      
24.021 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 RANDOM_EXCHANGES METAD TORSION INCLUDE PRINT DUMPFORCES bias generic colvar
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 CONSTANT CENTER CONTACTMAP ENDPLUMED TORSION METAINFERENCE RMSD PRINT WHOLEMOLECULES GYRATION FLUSH UPPER_WALLS PBMETAD MOLINFO isdb bias colvar generic vatom
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 METAD MOLINFO PATHMSD PRINT WHOLEMOLECULES MOVINGRESTRAINT LOWER_WALLS UPPER_WALLS CENTER DISTANCE bias generic colvar vatom
24.010 Modelling mechanobiological processes Claire Pritchard, Guillaume Stirnemann and Glen Hocky A tutorial on modelling mechanobiological processes Metadynamics, pulling, force, rates, GPCR RESTRAINT MATHEVAL METAD UNITS COMMITTOR PRINT BIASVALUE COM DUMPATOMS DISTANCE bias function setup colvar generic vatom
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 READ REWEIGHT_METAD METAD COORDINATION UNITS HISTOGRAM CUSTOM HBOND_MATRIX ANGLE PRINT GROUP UPPER_WALLS FLUSH DISTANCE DUMPGRID gridtools bias setup function adjmat colvar generic core
24.008 Using the maze module Jakub Rydzewski Sampling ligand-protein dissociation using the maze module protein, ligand, dissociation, unbinding, maze GROUP COMMITTOR CENTER DISTANCE colvar generic core 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 RESTRAINT METAD UNITS TORSION COORDINATION UPPER_WALLS EXTENDED_LAGRANGIAN PRINT WHOLEMOLECULES COM LOWER_WALLS GROUP DISTANCE FLUSH MOLINFO RESTART bias setup colvar generic vatom core
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 LESS_THAN METAD SUM DISTANCES PRINT FLUSH UPPER_WALLS COMBINE DISTANCE bias function colvar generic multicolvar
24.001 hybrid Small Angle Scattering — hands-on guide Federico Ballabio Practical guide to the use of the hySAS module.   RESTRAINT SAXS STATS PRINT BIASVALUE GYRATION ENSEMBLE MOLINFO isdb bias function colvar generic
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    
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    
22.017 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 PRINT BIASVALUE WHOLEMOLECULES GROUP EMMIVOX MOLINFO bias generic core isdb
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 RESTRAINT MATHEVAL METAD UNITS FISST PRINT BIASVALUE DUMPATOMS DISTANCE fisst bias function setup colvar generic
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 METAD UNITS PRINT LOWER_WALLS UPPER_WALLS DISTANCE bias colvar generic setup
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 MATRIX_VECTOR_PRODUCT CONTACT_MATRIX MORE_THAN RESTRAINT COORDINATIONNUMBER SUM CLUSTER_DISTRIBUTION CLUSTER_NATOMS ONES PRINT DFSCLUSTERING GROUP FLUSH bias function adjmat matrixtools generic clusters core symfunc
22.003 Rethinking Metadynamics using the OPES method Michele Invernizzi An introduction to the On-the-fly Probability Enhanced Sampling method masterclass-2022 ECV_MULTITHERMAL OPES_METAD_EXPLORE TORSION OPES_EXPANDED ECV_UMBRELLAS_LINE ENERGY OPES_METAD colvar opes
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 DUMPVECTOR LANDMARK_SELECT_FPS SKETCHMAP DUMPPDB CLASSICAL_MDS PATH GROUP ALPHARMSD MOLINFO PROJECT_POINTS PARABETARMSD COORDINATIONNUMBER COLLECT_FRAMES PCA PCAVARS DUMPGRID MORE_THAN TORSION HISTOGRAM PRINT ANTIBETARMSD UNITS COMMITTOR FCCUBIC RMSD DUMPMULTICOLVAR gridtools landmarks secondarystructure mapping function setup colvar generic multicolvar core symfunc dimred
21.003 Umbrella Sampling Giovanni Bussi How to calculate statistical averages and free energy surfaces using umbrella sampling masterclass-2021 RESTRAINT READ TORSION HISTOGRAM CUSTOM PRINT BIASVALUE REWEIGHT_BIAS CONVERT_TO_FES MOLINFO DUMPGRID gridtools bias function colvar generic
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 PARABETARMSD TORSION COMBINE PRINT WHOLEMOLECULES MOLINFO GYRATION ANTIBETARMSD ALPHARMSD DUMPATOMS CENTER DISTANCE secondarystructure function colvar generic vatom