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