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