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