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