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