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
24.020 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    
24.013 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 DISTANCE DUMPATOMS UNITS RESTRAINT METAD COM BIASVALUE COMMITTOR PRINT MATHEVAL function vatom bias setup generic colvar
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 GROUP COMBINE LESS_THAN UPPER_WALLS SUM DISTANCES CENTER PRINT METAD function vatom colvar bias generic multicolvar core
24.001 hybrid Small Angle Scattering — hands-on guide Federico Ballabio Practical guide to the use of the hySAS module.   GYRATION ENSEMBLE SAXS RESTRAINT BIASVALUE MOLINFO STATS PRINT function isdb bias generic colvar
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    
22.012 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 OPES_METAD GROUP DISTANCE_MATRIX UPPER_WALLS SUM ONES MEAN HISTOGRAM CUSTOM MORE_THAN MATHEVAL LOWER_WALLS DUMPGRID MATRIX_VECTOR_PRODUCT Q6 opes function envsim matrixtools adjmat bias generic symfunc gridtools core
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 PRINT MOLINFO generic colvar
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 GROUP COORDINATIONNUMBER PRINT DFSCLUSTERING CLUSTER_DISTRIBUTION MEAN ONES SUM CLUSTER_NATOMS CONTACT_MATRIX RESTRAINT MORE_THAN MATRIX_VECTOR_PRODUCT clusters function matrixtools adjmat bias generic symfunc core
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 PRINT TORSION pytorch generic colvar
21.005 Replica exchange methods Giovanni Bussi Running umbrella sampling with replica exchange, bias exchange metadynamics and parallel tempering metadynamics masterclass-2021 RESTRAINT TORSION MOLINFO RANDOM_EXCHANGES PRINT METAD generic bias colvar
21.004 Metadynamics Max Bonomi How to calculate statistical averages and free energy surfaces using metadynamics masterclass-2021 REWEIGHT_BIAS TORSION HISTOGRAM MOLINFO CONVERT_TO_FES DUMPGRID PRINT METAD generic gridtools bias 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 DISTANCE AVERAGE COORDINATIONNUMBER UPPER_WALLS REWEIGHT_BIAS UNITS CONSTANT RESTRAINT HISTOGRAM CUSTOM METAD COM CONVERT_TO_FES DUMPGRID PRINT READ function vatom bias setup generic symfunc gridtools colvar
20.001 Installing PLUMED Gareth Tribello An interactive tutorial resource on compiling PLUMED and linking it with MD codes.      
24.019 ASE-PLUMED interface Daniel Sucerquia, Pilar Cossio, Olga Lopez-Acevedo Using PLUMED from ASE atomistic calculations, ab-initio, molecular dynamics CUSTOM MATRIX_VECTOR_PRODUCT ONES COORDINATION PRINT METAD COMBINE FLUSH LOWER_WALLS MEAN COORDINATIONNUMBER UPPER_WALLS DISTANCE CONTACT_MATRIX COM GYRATION GROUP UNITS function adjmat bias setup symfunc core colvar vatom matrixtools generic
24.018 Permutation Invariant Vector and Water Crystallisation Silvio Pipolo, Fabio Pietrucci Modelling water crystallisation using PIV variables PIV, PathCV, Water Crystallisation PIV PLUMED CELL FUNCPATHMSD PRINT METAD LOWER_WALLS UPPER_WALLS function bias piv colvar generic
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 METAINFERENCE CONTACTMAP PBMETAD WHOLEMOLECULES PRINT TORSION FLUSH ENDPLUMED GYRATION CONSTANT RMSD UPPER_WALLS CENTER isdb bias colvar vatom 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 MOLINFO PATHMSD WHOLEMOLECULES MOVINGRESTRAINT PRINT METAD LOWER_WALLS UPPER_WALLS DISTANCE CENTER bias vatom colvar generic
24.008 Using the maze module Jakub Rydzewski Sampling ligand-protein dissociation using the maze module protein, ligand, dissociation, unbinding, maze COMMITTOR GROUP CENTER DISTANCE core vatom colvar 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 WHOLEMOLECULES KDE FLUSH WRAPAROUND RMSD COORDINATION POSITION GROUP DUMPGRID REWEIGHT_BIAS FIT_TO_TEMPLATE HISTOGRAM MATHEVAL ONES PRINT ACCUMULATE CUSTOM METAD RESTRAINT READ UPPER_WALLS COM CONVERT_TO_FES function bias gridtools core colvar vatom 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    
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 MOLINFO EMMIVOX WHOLEMOLECULES PRINT BIASVALUE GROUP isdb core bias generic
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 OPT_AVERAGED_SGD BF_WAVELETS REWEIGHT_BIAS PRINT DUMPGRID READ DISTANCE BF_LEGENDRE UPPER_WALLS COORDINATION TD_UNIFORM HISTOGRAM CONVERT_TO_FES TD_WELLTEMPERED ves bias gridtools 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 PRINT METAD LOWER_WALLS UPPER_WALLS DISTANCE UNITS colvar bias generic setup
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_UMBRELLAS_LINE ENERGY TORSION OPES_METAD_EXPLORE OPES_EXPANDED ECV_MULTITHERMAL colvar opes
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    
21.007 Optimizing PLUMED performances Max Bonomi Some lessons on monitoring and improving the performance of PLUMED and gromacs masterclass-2021 CUSTOM DEBUG EFFECTIVE_ENERGY_DRIFT WHOLEMOLECULES PRINT METAD DISTANCE RMSD COORDINATION COMBINE GROUP function bias core colvar generic
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 TORSION PROJECT_POINTS COMMITTOR LANDMARK_SELECT_FPS RMSD PARABETARMSD GROUP DUMPGRID SKETCHMAP DUMPMULTICOLVAR PCAVARS MORE_THAN PATH COLLECT_FRAMES UNITS HISTOGRAM DUMPVECTOR CLASSICAL_MDS PRINT FCCUBIC ANTIBETARMSD ALPHARMSD PCA COORDINATIONNUMBER DUMPPDB secondarystructure function setup dimred mapping symfunc multicolvar core gridtools landmarks colvar 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 METAD DUMPFORCES PRINT TORSION INCLUDE RANDOM_EXCHANGES colvar bias generic
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 UPPER_WALLS METAD DISTANCES PRINT COORDINATION GROUP LOWER_WALLS BIASVALUE CUSTOM core bias generic function colvar multicolvar
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_METAD_EXPLORE UPPER_WALLS ENERGY PRINT CENTER GROUP MATHEVAL COORDINATION ECV_MULTITHERMAL FIXEDATOM OPES_EXPANDED ANGLE FIT_TO_TEMPLATE LOWER_WALLS WHOLEMOLECULES core opes bias generic vatom function colvar
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 colvar setup generic
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
24.009 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 DISTANCE UPPER_WALLS METAD DUMPGRID HBOND_MATRIX PRINT GROUP COORDINATION UNITS HISTOGRAM REWEIGHT_METAD READ CUSTOM FLUSH ANGLE core gridtools adjmat bias generic function setup colvar
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 DISTANCE UPPER_WALLS METAD RESTART PRINT TORSION MOLINFO UNITS GROUP COM COORDINATION EXTENDED_LAGRANGIAN LOWER_WALLS RESTRAINT FLUSH WHOLEMOLECULES core bias generic vatom setup colvar
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 DISTANCE UPPER_WALLS METAD RESTART PRINT UNITS FIXEDATOM LOWER_WALLS BIASVALUE CUSTOM FLUSH bias generic vatom function setup colvar
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 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 DISTANCE METAD FISST PRINT MATHEVAL UNITS DUMPATOMS RESTRAINT BIASVALUE bias generic function setup fisst 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 SUM ANTIBETARMSD PRINT PARABETARMSD MOLINFO LOWEST BIASVALUE SECONDARY_STRUCTURE_RMSD SASA_HASEL LESS_THAN GYRATION ALPHARMSD secondarystructure sasa bias generic function colvar
21.003 Umbrella Sampling Giovanni Bussi How to calculate statistical averages and free energy surfaces using umbrella sampling masterclass-2021 DUMPGRID PRINT TORSION MOLINFO HISTOGRAM CONVERT_TO_FES REWEIGHT_BIAS RESTRAINT READ BIASVALUE CUSTOM gridtools bias generic function colvar
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 DISTANCE ANTIBETARMSD PRINT CENTER MOLINFO TORSION PARABETARMSD DUMPATOMS GYRATION ALPHARMSD WHOLEMOLECULES secondarystructure generic vatom function 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.   CONSTANT TORSION BIASVALUE PRINT PBMETAD MATHEVAL WHOLEMOLECULES bias colvar generic function
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 MATRIX_VECTOR_PRODUCT GPATH DISTANCE_MATRIX MATRIX_PRODUCT TORSION INTERPOLATE_GRID CLUSTER_PROPERTIES OUTER_PRODUCT VOLUME PRINT SPRINT VSTACK CLUSTER_WEIGHTS RDF EUCLIDEAN_DISTANCE GEOMETRIC_PATH Q6 CONSTANT COORDINATIONNUMBER SORT COM DFSCLUSTERING PDB2CONSTANT MEAN BIASVALUE LESS_THAN DISTANCES DIAGONALIZE SUM DUMPGRID RMSD Q1 GROUP GSYMFUNC_THREEBODY MORE_THAN REFERENCE_GRID PAIRENTROPY KDE RESTRAINT CONTACT_MATRIX PCAVARS GATHER_REPLICAS CONCATENATE ACCUMULATE Q4 LOCAL_AVERAGE FIXEDATOM LOWEST HISTOGRAM CUSTOM DISPLACEMENT DIFFERENCE SELECT_COMPONENTS INTEGRATE_GRID DISTANCE CENTER AVERAGE COMBINE ONES LOCAL_Q1 INSPHERE PATH RMSD_VECTOR SPHERICAL_HARMONIC WHOLEMOLECULES POSITION TRANSPOSE symfunc matrixtools gridtools sprint valtools bias clusters mapping vatom colvar generic refdist multicolvar core adjmat function volumes
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 MATHEVAL MOLINFO TORSION DISTANCE BIASVALUE PRINT EDS bias eds colvar generic function