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