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 |
|---|---|---|---|---|---|---|
| 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 | |||
| 24.015 | 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 | PRINT DISTANCE LOAD | generic setup colvar |
| 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 | CONSTANT MOLINFO GYRATION FLUSH TORSION PRINT CONTACTMAP METAINFERENCE CENTER ENDPLUMED WHOLEMOLECULES RMSD UPPER_WALLS PBMETAD | vatom isdb bias generic colvar |
| 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 | generic setup |
| 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 | LOWER_WALLS MOLINFO METAD PATHMSD PRINT CENTER DISTANCE WHOLEMOLECULES MOVINGRESTRAINT UPPER_WALLS | vatom generic 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 | MOLINFO EMMIVOX PRINT WHOLEMOLECULES BIASVALUE GROUP | isdb generic core bias |
| 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 LOWER_WALLS UPPER_WALLS SUM MORE_THAN OPES_METAD DUMPGRID MATHEVAL HISTOGRAM DISTANCE_MATRIX MEAN Q6 MATRIX_VECTOR_PRODUCT ENVIRONMENTSIMILARITY GROUP ONES | core adjmat opes generic gridtools bias envsim function matrixtools symfunc |
| 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 | LOWER_WALLS METAD PRINT DISTANCE UNITS UPPER_WALLS | generic setup colvar bias |
| 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 PRINT TORSION | pytorch generic colvar |
| 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 METAD COMBINE COORDINATION PRINT EFFECTIVE_ENERGY_DRIFT DISTANCE WHOLEMOLECULES RMSD GROUP | generic bias function colvar core |
| 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 | MORE_THAN DUMPPDB UNITS PCA TORSION PROJECT_POINTS DUMPVECTOR ANTIBETARMSD LANDMARK_SELECT_FPS MOLINFO DUMPGRID SKETCHMAP PRINT PCAVARS HISTOGRAM COMMITTOR PARABETARMSD CLASSICAL_MDS GROUP DUMPMULTICOLVAR COORDINATIONNUMBER ALPHARMSD COLLECT_FRAMES PATH FCCUBIC RMSD | mapping symfunc dimred generic gridtools multicolvar setup secondarystructure landmarks function colvar core |
| 21.003 | Umbrella Sampling | Giovanni Bussi | How to calculate statistical averages and free energy surfaces using umbrella sampling | masterclass-2021 | CUSTOM MOLINFO TORSION DUMPGRID RESTRAINT HISTOGRAM PRINT CONVERT_TO_FES READ BIASVALUE REWEIGHT_BIAS | generic gridtools 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 | CUSTOM REWEIGHT_BIAS CONSTANT COM METAD DUMPGRID RESTRAINT HISTOGRAM PRINT AVERAGE CONVERT_TO_FES COORDINATIONNUMBER READ DISTANCE UNITS UPPER_WALLS | vatom generic gridtools setup bias function colvar symfunc |
| 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 | CONTACT_MATRIX LOWER_WALLS UNITS ONES MATRIX_VECTOR_PRODUCT PRINT COM UPPER_WALLS METAD FLUSH GYRATION COORDINATIONNUMBER CUSTOM GROUP COORDINATION MEAN DISTANCE COMBINE | core bias adjmat matrixtools setup generic vatom function colvar symfunc |
| 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 | LOWER_WALLS UPPER_WALLS METAD PRINT CUSTOM BIASVALUE COORDINATION GROUP DISTANCES | bias generic function multicolvar colvar core |
| 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 | DUMPGRID UNITS READ ANGLE UPPER_WALLS METAD PRINT HISTOGRAM FLUSH CUSTOM REWEIGHT_METAD GROUP COORDINATION HBOND_MATRIX DISTANCE | bias adjmat setup generic function colvar core gridtools |
| 24.008 | Using the maze module | Jakub Rydzewski | Sampling ligand-protein dissociation using the maze module | protein, ligand, dissociation, unbinding, maze | CENTER COMMITTOR GROUP DISTANCE | colvar core generic 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 | LOWER_WALLS UNITS UPPER_WALLS PRINT METAD FLUSH FIXEDATOM CUSTOM BIASVALUE RESTART DISTANCE | bias setup generic vatom function 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 | UPPER_WALLS METAD PRINT FLUSH DISTANCES LESS_THAN COMBINE DISTANCE SUM | colvar bias generic function multicolvar |
| 24.001 | hybrid Small Angle Scattering — hands-on guide | Federico Ballabio | Practical guide to the use of the hySAS module. | STATS PRINT GYRATION MOLINFO RESTRAINT BIASVALUE SAXS ENSEMBLE | bias generic function isdb 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_RMSD PARABETARMSD SASA_HASEL PRINT LOWEST GYRATION MOLINFO ANTIBETARMSD BIASVALUE ALPHARMSD LESS_THAN SUM | bias sasa generic function colvar secondarystructure |
| 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 MOLINFO TORSION | 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 PRINT MOLINFO BIASVALUE MATHEVAL DISTANCE TORSION | eds bias generic function colvar |
| 22.003 | Rethinking Metadynamics using the OPES method | Michele Invernizzi | An introduction to the On-the-fly Probability Enhanced Sampling method | masterclass-2022 | ECV_UMBRELLAS_LINE OPES_EXPANDED OPES_METAD ENERGY OPES_METAD_EXPLORE ECV_MULTITHERMAL 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 | PRINT METAD MOLINFO RESTRAINT RANDOM_EXCHANGES TORSION | colvar bias generic |
| 21.004 | Metadynamics | Max Bonomi | How to calculate statistical averages and free energy surfaces using metadynamics | masterclass-2021 | DUMPGRID HISTOGRAM PRINT METAD MOLINFO REWEIGHT_BIAS CONVERT_TO_FES TORSION | colvar bias gridtools generic |
| 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 | PARABETARMSD PRINT GYRATION CENTER MOLINFO ANTIBETARMSD DUMPATOMS ALPHARMSD WHOLEMOLECULES COMBINE DISTANCE TORSION | generic vatom function colvar secondarystructure |
| 20.001 | Installing PLUMED | Gareth Tribello | An interactive tutorial resource on compiling PLUMED and linking it with MD codes. | |||
| 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 | RANDOM_EXCHANGES PRINT DUMPFORCES INCLUDE TORSION METAD | colvar bias generic |
| 24.018 | Permutation Invariant Vector and Water Crystallisation | Silvio Pipolo, Fabio Pietrucci | Modelling water crystallisation using PIV variables | PIV, PathCV, Water Crystallisation | PRINT CELL LOWER_WALLS PIV METAD UPPER_WALLS PLUMED FUNCPATHMSD | function colvar piv bias 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 | MATHEVAL FIT_TO_TEMPLATE FIXEDATOM LOWER_WALLS PRINT CENTER WHOLEMOLECULES ANGLE OPES_METAD_EXPLORE UPPER_WALLS GROUP ENERGY OPES_EXPANDED DISTANCE ECV_MULTITHERMAL COORDINATION | core opes function colvar vatom bias generic |
| 24.010 | Modelling mechanobiological processes | Claire Pritchard, Guillaume Stirnemann and Glen Hocky | A tutorial on modelling mechanobiological processes | Metadynamics, pulling, force, rates, GPCR | PRINT MATHEVAL RESTRAINT METAD COM DISTANCE DUMPATOMS COMMITTOR UNITS BIASVALUE | function setup colvar vatom bias 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 | MOLINFO PRINT COORDINATION RESTART LOWER_WALLS WHOLEMOLECULES EXTENDED_LAGRANGIAN FLUSH RESTRAINT TORSION METAD GROUP COM DISTANCE UPPER_WALLS UNITS | core setup colvar vatom bias 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 | MATHEVAL FIT_TO_TEMPLATE PRINT WHOLEMOLECULES RESTRAINT READ GROUP COM ACCUMULATE REWEIGHT_BIAS FLUSH DUMPGRID HISTOGRAM CUSTOM COORDINATION WRAPAROUND UPPER_WALLS POSITION KDE RMSD METAD ONES CONVERT_TO_FES | core function colvar vatom gridtools bias 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 | PRINT COORDINATION FLUSH | 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. | MATHEVAL PRINT WHOLEMOLECULES TORSION CONSTANT BIASVALUE PBMETAD | colvar bias function 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 | ||
| 22.015 | 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 | MATHEVAL PRINT FISST RESTRAINT METAD DISTANCE DUMPATOMS UNITS BIASVALUE | function setup colvar fisst 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 | PRINT OPT_AVERAGED_SGD VES_LINEAR_EXPANSION REWEIGHT_BIAS BF_LEGENDRE DUMPGRID READ UPPER_WALLS HISTOGRAM DISTANCE TD_UNIFORM CONVERT_TO_FES COORDINATION TD_WELLTEMPERED BF_WAVELETS | ves colvar gridtools 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 | PRINT DFSCLUSTERING SUM MEAN FLUSH COORDINATIONNUMBER RESTRAINT CLUSTER_DISTRIBUTION GROUP MORE_THAN CONTACT_MATRIX ONES CLUSTER_NATOMS MATRIX_VECTOR_PRODUCT | core matrixtools function adjmat bias generic symfunc clusters |
| 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 SORT PRINT COORDINATIONNUMBER RMSD KDE INTERPOLATE_GRID LOCAL_AVERAGE SELECT_COMPONENTS SPHERICAL_HARMONIC DISTANCE_MATRIX DISTANCES MATRIX_PRODUCT REFERENCE_GRID RMSD_VECTOR VSTACK PCAVARS DFSCLUSTERING CONTACT_MATRIX ONES BIASVALUE PATH FIXEDATOM MEAN WHOLEMOLECULES LOWEST Q1 ACCUMULATE CLUSTER_PROPERTIES CONCATENATE Q6 LOCAL_Q1 COM DIFFERENCE GEOMETRIC_PATH GATHER_REPLICAS MATRIX_VECTOR_PRODUCT CLUSTER_WEIGHTS TORSION Q4 HISTOGRAM DISPLACEMENT RESTRAINT PDB2CONSTANT DIAGONALIZE DOMAIN_DECOMPOSITION INTEGRATE_GRID POSITION LESS_THAN INSPHERE TRANSPOSE DUMPGRID MORE_THAN CENTER AVERAGE OUTER_PRODUCT SUM DISTANCE COMBINE VOLUME EUCLIDEAN_DISTANCE PAIRENTROPY SPRINT RDF GPATH CONSTANT GROUP GSYMFUNC_THREEBODY | generic adjmat volumes sprint matrixtools vatom function colvar mapping gridtools refdist bias multicolvar symfunc core valtools clusters |