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