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
24.020 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    
24.015 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 colvar setup 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    
24.005 Path integral metadynamics Guillaume Fraux and Michele Ceriotti Incorporating nuclear quantum effects in metadynamics simulations using path integrals Metadynamics, path integrals, nuclear quantum effects DISTANCE PRINT SUM METAD DISTANCES FLUSH COMBINE UPPER_WALLS LESS_THAN multicolvar colvar bias function 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 PRINT METAD ONES READ MATHEVAL COM RESTRAINT GROUP RMSD CONVERT_TO_FES HISTOGRAM KDE FIT_TO_TEMPLATE FLUSH ACCUMULATE WRAPAROUND POSITION CUSTOM WHOLEMOLECULES REWEIGHT_BIAS COORDINATION UPPER_WALLS DUMPGRID vatom core colvar bias function generic gridtools
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    
22.013 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 ALPHARMSD DISTANCE GYRATION PARABETARMSD PRINT SUM ANTIBETARMSD LOWEST MOLINFO BIASVALUE CUSTOM SASA_HASEL SECONDARY_STRUCTURE_DRMSD LESS_THAN colvar bias sasa secondarystructure 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 MATRIX_VECTOR_PRODUCT OPES_METAD GROUP LOWER_WALLS SUM DISTANCE_MATRIX ONES CUSTOM MEAN ENVIRONMENTSIMILARITY MATHEVAL Q6 UPPER_WALLS DUMPGRID MORE_THAN HISTOGRAM core adjmat envsim bias opes gridtools symfunc function generic matrixtools
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 PRINT SKETCHMAP COLLECT_FRAMES FCCUBIC COMMITTOR UNITS GROUP PROJECT_POINTS PCAVARS DUMPMULTICOLVAR RMSD DUMPVECTOR CLASSICAL_MDS HISTOGRAM ALPHARMSD MOLINFO DUMPPDB MORE_THAN PARABETARMSD LANDMARK_SELECT_FPS TORSION ANTIBETARMSD PCA DUMPGRID PATH COORDINATIONNUMBER core setup multicolvar colvar landmarks mapping secondarystructure symfunc function generic dimred gridtools
21.005 Replica exchange methods Giovanni Bussi Running umbrella sampling with replica exchange, bias exchange metadynamics and parallel tempering metadynamics masterclass-2021 RANDOM_EXCHANGES PRINT TORSION METAD MOLINFO RESTRAINT colvar bias generic
21.003 Umbrella Sampling Giovanni Bussi How to calculate statistical averages and free energy surfaces using umbrella sampling masterclass-2021 TORSION PRINT MOLINFO READ CUSTOM BIASVALUE CONVERT_TO_FES REWEIGHT_BIAS DUMPGRID RESTRAINT HISTOGRAM colvar bias function generic gridtools
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 GROUP LOWER_WALLS METAD DISTANCES BIASVALUE CUSTOM UPPER_WALLS COORDINATION PRINT generic multicolvar bias core function 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 ANGLE GROUP MATHEVAL LOWER_WALLS ENERGY ECV_MULTITHERMAL CENTER DISTANCE FIT_TO_TEMPLATE FIXEDATOM UPPER_WALLS COORDINATION WHOLEMOLECULES OPES_METAD_EXPLORE PRINT OPES_EXPANDED generic bias core opes vatom function colvar
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
24.008 Using the maze module Jakub Rydzewski Sampling ligand-protein dissociation using the maze module protein, ligand, dissociation, unbinding, maze COMMITTOR DISTANCE CENTER GROUP vatom core generic 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 GROUP LOWER_WALLS RESTART UNITS METAD COORDINATION MOLINFO DISTANCE FLUSH EXTENDED_LAGRANGIAN UPPER_WALLS COM TORSION RESTRAINT WHOLEMOLECULES PRINT generic bias core vatom setup colvar
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 COORDINATION PRINT FLUSH generic colvar
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 MATHEVAL BIASVALUE TORSION WHOLEMOLECULES PBMETAD PRINT function generic colvar bias
24.001 hybrid Small Angle Scattering — hands-on guide Federico Ballabio Practical guide to the use of the hySAS module.   STATS SAXS MOLINFO GYRATION BIASVALUE ENSEMBLE RESTRAINT PRINT generic bias function isdb colvar
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 GROUP EMMIVOX MOLINFO BIASVALUE WHOLEMOLECULES PRINT generic isdb core bias
22.011 Variationally Enhanced Sampling Omar Valsson An introduction to running Variationally Enhanced Sampling (VES) using PLUMED. masterclass-2022 Variationally Enhanced Sampling VES CONVERT_TO_FES HISTOGRAM BF_LEGENDRE REWEIGHT_BIAS BF_WAVELETS DISTANCE READ DUMPGRID TD_WELLTEMPERED UPPER_WALLS COORDINATION OPT_AVERAGED_SGD VES_LINEAR_EXPANSION TD_UNIFORM PRINT ves generic gridtools bias colvar
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 COORDINATIONNUMBER GROUP CLUSTER_NATOMS MATRIX_VECTOR_PRODUCT RESTRAINT FLUSH CONTACT_MATRIX DFSCLUSTERING MORE_THAN SUM ONES PRINT CLUSTER_DISTRIBUTION generic matrixtools bias adjmat clusters core function symfunc
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 MATHEVAL MOLINFO DISTANCE BIASVALUE EDS TORSION PRINT generic bias eds function colvar
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 ECV_MULTITHERMAL ENERGY TORSION OPES_METAD OPES_METAD_EXPLORE OPES_EXPANDED colvar opes
21.004 Metadynamics Max Bonomi How to calculate statistical averages and free energy surfaces using metadynamics masterclass-2021 CONVERT_TO_FES HISTOGRAM REWEIGHT_BIAS METAD MOLINFO DUMPGRID TORSION PRINT generic gridtools colvar bias
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 CONVERT_TO_FES HISTOGRAM CONSTANT COORDINATIONNUMBER UNITS REWEIGHT_BIAS METAD DISTANCE READ RESTRAINT DUMPGRID CUSTOM UPPER_WALLS COM AVERAGE PRINT generic colvar gridtools bias vatom function setup symfunc
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 INCLUDE RANDOM_EXCHANGES PRINT DUMPFORCES TORSION METAD colvar bias generic
24.019 ASE-PLUMED interface Daniel Sucerquia, Pilar Cossio, Olga Lopez-Acevedo Using PLUMED from ASE atomistic calculations, ab-initio, molecular dynamics DISTANCE GYRATION CONTACT_MATRIX METAD COORDINATION COMBINE COORDINATIONNUMBER ONES COM CUSTOM MATRIX_VECTOR_PRODUCT PRINT LOWER_WALLS UNITS UPPER_WALLS GROUP FLUSH MEAN colvar function symfunc setup matrixtools generic adjmat core vatom bias
24.018 Permutation Invariant Vector and Water Crystallisation Silvio Pipolo, Fabio Pietrucci Modelling water crystallisation using PIV variables PIV, PathCV, Water Crystallisation CELL FUNCPATHMSD PRINT LOWER_WALLS UPPER_WALLS METAD PIV colvar piv function generic bias
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 PBMETAD GYRATION CENTER CONTACTMAP ENDPLUMED CONSTANT MOLINFO PRINT METAINFERENCE TORSION RMSD UPPER_WALLS WHOLEMOLECULES FLUSH colvar generic isdb vatom bias
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 PATHMSD CENTER MOVINGRESTRAINT MOLINFO PRINT LOWER_WALLS UPPER_WALLS WHOLEMOLECULES DISTANCE vatom colvar bias generic
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 METAD COORDINATION HISTOGRAM FLUSH ANGLE READ PRINT REWEIGHT_METAD UNITS UPPER_WALLS DUMPGRID CUSTOM HBOND_MATRIX GROUP DISTANCE colvar gridtools function setup generic adjmat core 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 METAD RESTART FLUSH LOWER_WALLS PRINT UNITS BIASVALUE CUSTOM UPPER_WALLS FIXEDATOM DISTANCE colvar function setup generic vatom bias
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    
22.015 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 DUMPATOMS PRINT FISST MATHEVAL BIASVALUE UNITS METAD DISTANCE colvar function setup generic fisst 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 PRINT MOLINFO 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 PRINT UNITS UPPER_WALLS LOWER_WALLS DISTANCE setup colvar bias generic
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 PRINT PYTORCH_MODEL colvar pytorch 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    
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    
21.001 PLUMED syntax and analysis Max Bonomi Basic features of the PLUMED input syntax with a particular focus on PBCs and selection tools masterclass-2021 GYRATION ALPHARMSD COMBINE CENTER ANTIBETARMSD MOLINFO DUMPATOMS PRINT TORSION PARABETARMSD WHOLEMOLECULES DISTANCE colvar function secondarystructure generic vatom
20.001 Installing PLUMED Gareth Tribello An interactive tutorial resource on compiling PLUMED and linking it with MD codes.      
24.010 Modelling mechanobiological processes Claire Pritchard, Guillaume Stirnemann and Glen Hocky A tutorial on modelling mechanobiological processes Metadynamics, pulling, force, rates, GPCR COMMITTOR RESTRAINT DISTANCE PRINT DUMPATOMS COM MATHEVAL BIASVALUE METAD UNITS colvar bias vatom function generic setup
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   Q4 TORSION CLUSTER_WEIGHTS RESTRAINT KDE LOCAL_AVERAGE DIFFERENCE MATRIX_PRODUCT PRINT OUTER_PRODUCT CUSTOM PDB2CONSTANT LESS_THAN CONCATENATE GATHER_REPLICAS DFSCLUSTERING PATH INSPHERE RMSD_VECTOR COM SPRINT DISTANCE CONTACT_MATRIX MATRIX_VECTOR_PRODUCT COMBINE RMSD ONES GSYMFUNC_THREEBODY GEOMETRIC_PATH POSITION GET_VOLUME_ELEMENT LOCAL_Q1 HISTOGRAM Q1 DIAGONALIZE REFERENCE_GRID EUCLIDEAN_DISTANCE CLUSTER_PROPERTIES DISPLACEMENT SPHERICAL_HARMONIC DOMAIN_DECOMPOSITION PAIRENTROPY LOWEST AVERAGE RDF Q6 INTERPOLATE_GRID PCAVARS INTEGRATE_GRID COORDINATIONNUMBER WHOLEMOLECULES VSTACK DUMPGRID SELECT_COMPONENTS SUM CENTER VOLUME FIXEDATOM MORE_THAN CONSTANT GROUP MEAN BIASVALUE ACCUMULATE DISTANCE_MATRIX DISTANCES GPATH SORT TRANSPOSE colvar sprint core multicolvar bias adjmat vatom volumes refdist function matrixtools clusters generic valtools symfunc mapping gridtools
21.007 Optimizing PLUMED performances Max Bonomi Some lessons on monitoring and improving the performance of PLUMED and gromacs masterclass-2021 COORDINATION DISTANCE EFFECTIVE_ENERGY_DRIFT RMSD COMBINE PRINT DEBUG CUSTOM GROUP METAD WHOLEMOLECULES colvar core bias function generic