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