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