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
25.001 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      
24.014 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 UPPER_WALLS CONTACTMAP CENTER GYRATION PRINT PBMETAD ENDPLUMED TORSION CONSTANT METAINFERENCE FLUSH WHOLEMOLECULES MOLINFO vatom isdb colvar bias generic
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    
24.003 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 PRINT COORDINATION colvar 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 MEAN SUM ONES Q6 UPPER_WALLS MATRIX_VECTOR_PRODUCT DISTANCE_MATRIX HISTOGRAM ENVIRONMENTSIMILARITY MORE_THAN LOWER_WALLS DUMPGRID OPES_METAD GROUP CUSTOM MATHEVAL envsim adjmat function opes symfunc matrixtools core bias generic gridtools
22.011 Variationally Enhanced Sampling Omar Valsson An introduction to running Variationally Enhanced Sampling (VES) using PLUMED. masterclass-2022 Variationally Enhanced Sampling VES BF_WAVELETS COORDINATION UPPER_WALLS VES_LINEAR_EXPANSION HISTOGRAM REWEIGHT_BIAS OPT_AVERAGED_SGD DUMPGRID READ TD_UNIFORM TD_WELLTEMPERED BF_LEGENDRE CONVERT_TO_FES PRINT DISTANCE colvar bias generic gridtools ves
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    
21.006 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 UNITS PCA PCAVARS ANTIBETARMSD COORDINATIONNUMBER MOLINFO DUMPVECTOR COLLECT_FRAMES SKETCHMAP FCCUBIC MORE_THAN TORSION DUMPPDB LANDMARK_SELECT_FPS PATH RMSD CLASSICAL_MDS ALPHARMSD PROJECT_POINTS DUMPMULTICOLVAR HISTOGRAM COMMITTOR DUMPGRID PARABETARMSD GROUP PRINT secondarystructure function dimred multicolvar symfunc colvar landmarks core generic gridtools setup mapping
21.003 Umbrella Sampling Giovanni Bussi How to calculate statistical averages and free energy surfaces using umbrella sampling masterclass-2021 HISTOGRAM REWEIGHT_BIAS DUMPGRID TORSION CUSTOM READ RESTRAINT CONVERT_TO_FES PRINT MOLINFO BIASVALUE function colvar bias generic gridtools
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      
24.019 ASE-PLUMED interface Daniel Sucerquia, Pilar Cossio, Olga Lopez-Acevedo Using PLUMED from ASE atomistic calculations, ab-initio, molecular dynamics COMBINE CUSTOM DISTANCE COORDINATIONNUMBER GROUP MEAN GYRATION UNITS METAD PRINT CONTACT_MATRIX FLUSH COORDINATION MATRIX_VECTOR_PRODUCT ONES LOWER_WALLS UPPER_WALLS COM adjmat vatom function colvar core generic setup symfunc bias matrixtools
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 PRINT DISTANCE generic colvar setup
24.010 Modelling mechanobiological processes Claire Pritchard, Guillaume Stirnemann and Glen Hocky A tutorial on modelling mechanobiological processes Metadynamics, pulling, force, rates, GPCR RESTRAINT DISTANCE BIASVALUE COMMITTOR UNITS METAD PRINT MATHEVAL DUMPATOMS COM vatom function colvar generic setup bias
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 HISTOGRAM DISTANCE GROUP UNITS REWEIGHT_METAD DUMPGRID METAD PRINT FLUSH COORDINATION HBOND_MATRIX ANGLE READ UPPER_WALLS adjmat gridtools function colvar core generic setup bias
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 CUSTOM DISTANCE BIASVALUE FIXEDATOM RESTART UNITS METAD PRINT FLUSH LOWER_WALLS UPPER_WALLS vatom function colvar generic setup 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 PRINT READ GROUP RMSD METAD FIT_TO_TEMPLATE RESTRAINT CONVERT_TO_FES DUMPGRID COORDINATION WHOLEMOLECULES UPPER_WALLS REWEIGHT_BIAS POSITION WRAPAROUND FLUSH MATHEVAL COM gridtools vatom colvar function core 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.   PBMETAD BIASVALUE CONSTANT PRINT MATHEVAL TORSION WHOLEMOLECULES bias generic 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 DISTANCE UNITS METAD PRINT LOWER_WALLS UPPER_WALLS colvar generic bias 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 MORE_THAN CLUSTER_NATOMS RESTRAINT CLUSTER_DISTRIBUTION COORDINATIONNUMBER DFSCLUSTERING GROUP PRINT CONTACT_MATRIX FLUSH MATRIX_VECTOR_PRODUCT ONES SUM adjmat function clusters core generic symfunc bias matrixtools
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 EDS BIASVALUE DISTANCE PRINT MOLINFO MATHEVAL TORSION function colvar eds generic bias
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_EXPLORE ECV_MULTITHERMAL OPES_EXPANDED OPES_METAD TORSION ECV_UMBRELLAS_LINE ENERGY colvar opes
21.005 Replica exchange methods Giovanni Bussi Running umbrella sampling with replica exchange, bias exchange metadynamics and parallel tempering metadynamics masterclass-2021 RESTRAINT METAD MOLINFO PRINT TORSION RANDOM_EXCHANGES bias generic colvar
20.001 Installing PLUMED Gareth Tribello An interactive tutorial resource on compiling PLUMED and linking it with MD codes.      
24.018 Permutation Invariant Vector and Water Crystallisation Silvio Pipolo, Fabio Pietrucci Modelling water crystallisation using PIV variables PIV, PathCV, Water Crystallisation FUNCPATHMSD UPPER_WALLS METAD LOWER_WALLS PRINT CELL PIV colvar bias piv generic function
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
24.007 Transition-Tempered Metadynamics Jiangbo Wu and Gregory A. Voth An introduction to the transition tempered metadynamics method metadynamics, free energy sampling, reaction mechanism UNITS EXTENDED_LAGRANGIAN RESTART RESTRAINT TORSION DISTANCE FLUSH MOLINFO UPPER_WALLS METAD COORDINATION GROUP PRINT WHOLEMOLECULES COM LOWER_WALLS colvar bias setup generic core vatom
24.001 hybrid Small Angle Scattering — hands-on guide Federico Ballabio Practical guide to the use of the hySAS module.   SAXS RESTRAINT STATS ENSEMBLE MOLINFO PRINT BIASVALUE GYRATION colvar bias isdb 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    
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   DUMPGRID INTERPOLATE_GRID MATRIX_PRODUCT RMSD DISTANCE_MATRIX CLUSTER_PROPERTIES DISTANCE REFERENCE_GRID PAIRENTROPY EUCLIDEAN_DISTANCE INTEGRATE_GRID OUTER_PRODUCT VSTACK WHOLEMOLECULES COM COORDINATIONNUMBER LOCAL_Q1 DISPLACEMENT DIFFERENCE Q4 ACCUMULATE KDE SPHERICAL_HARMONIC PATH RDF GET_VOLUME_ELEMENT CUSTOM SPRINT DISTANCES GROUP BIASVALUE DFSCLUSTERING CLUSTER_WEIGHTS RMSD_VECTOR GSYMFUNC_THREEBODY CONSTANT AVERAGE Q6 DOMAIN_DECOMPOSITION LOWEST COMBINE SELECT_COMPONENTS HISTOGRAM SUM INSPHERE CONTACT_MATRIX ONES PDB2CONSTANT MEAN CONCATENATE LESS_THAN Q1 TRANSPOSE GATHER_REPLICAS MATRIX_VECTOR_PRODUCT VOLUME RESTRAINT PCAVARS MORE_THAN TORSION DIAGONALIZE GEOMETRIC_PATH POSITION FIXEDATOM LOCAL_AVERAGE GPATH SORT PRINT CENTER gridtools colvar matrixtools symfunc multicolvar bias sprint volumes refdist generic vatom core valtools function mapping clusters adjmat
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 valtools bias metatomic
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 PRINT BAIES BIASVALUE bias isdb generic core
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 PRINT RANDOM_EXCHANGES INCLUDE METAD DUMPFORCES TORSION bias colvar generic
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    
24.017 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 UPPER_WALLS PRINT CUSTOM COORDINATION METAD LOWER_WALLS BIASVALUE GROUP DISTANCES bias function generic core colvar multicolvar
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 MATHEVAL UPPER_WALLS CENTER PRINT WHOLEMOLECULES DISTANCE COORDINATION FIT_TO_TEMPLATE FIXEDATOM OPES_METAD_EXPLORE ECV_MULTITHERMAL LOWER_WALLS ENERGY ANGLE GROUP OPES_EXPANDED bias function generic core vatom opes colvar
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 UPPER_WALLS PRINT CENTER DISTANCE WHOLEMOLECULES METAD PATHMSD LOWER_WALLS MOVINGRESTRAINT MOLINFO bias vatom colvar generic
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 vatom generic 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 UPPER_WALLS PRINT DISTANCE FLUSH METAD LESS_THAN SUM COMBINE DISTANCES bias function generic colvar multicolvar
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 EMMIVOX WHOLEMOLECULES BIASVALUE MOLINFO GROUP bias isdb generic core
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 MATHEVAL PRINT DUMPATOMS DISTANCE UNITS METAD BIASVALUE RESTRAINT FISST bias setup fisst function generic colvar
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 ANTIBETARMSD PRINT ALPHARMSD SASA_HASEL DISTANCE CUSTOM LOWEST GYRATION LESS_THAN SUM BIASVALUE MOLINFO SECONDARY_STRUCTURE_DRMSD PARABETARMSD bias sasa secondarystructure function generic colvar
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 PRINT TORSION MOLINFO colvar 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 PRINT TORSION PYTORCH_MODEL colvar pytorch generic
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 DISTANCE COORDINATION WHOLEMOLECULES CUSTOM EFFECTIVE_ENERGY_DRIFT METAD RMSD DEBUG COMBINE GROUP bias function generic core colvar
21.004 Metadynamics Max Bonomi How to calculate statistical averages and free energy surfaces using metadynamics masterclass-2021 PRINT HISTOGRAM DUMPGRID CONVERT_TO_FES METAD REWEIGHT_BIAS MOLINFO TORSION bias colvar gridtools generic
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 UPPER_WALLS PRINT COORDINATIONNUMBER HISTOGRAM DUMPGRID CUSTOM CONVERT_TO_FES DISTANCE UNITS READ REWEIGHT_BIAS METAD CONSTANT AVERAGE COM RESTRAINT bias setup function gridtools symfunc generic vatom 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 ANTIBETARMSD PRINT CENTER ALPHARMSD DUMPATOMS DISTANCE WHOLEMOLECULES GYRATION COMBINE MOLINFO TORSION PARABETARMSD secondarystructure function generic vatom colvar