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 |
---|---|---|---|---|---|---|
24.017 | 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 METAD PRINT COORDINATION LOWER_WALLS CUSTOM BIASVALUE DISTANCES UPPER_WALLS | multicolvar colvar function bias core 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 | GROUP WHOLEMOLECULES FIXEDATOM PRINT OPES_METAD_EXPLORE OPES_EXPANDED MATHEVAL FIT_TO_TEMPLATE COORDINATION LOWER_WALLS ANGLE CENTER ENERGY ECV_MULTITHERMAL DISTANCE UPPER_WALLS | opes colvar function vatom bias core 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 | ENDPLUMED METAINFERENCE WHOLEMOLECULES GYRATION CONSTANT RMSD PRINT FLUSH CENTER PBMETAD CONTACTMAP TORSION MOLINFO UPPER_WALLS | isdb colvar bias vatom 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 | ||
24.012 | 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 |
24.009 | 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 METAD HBOND_MATRIX READ DUMPGRID PRINT REWEIGHT_METAD FLUSH COORDINATION CUSTOM ANGLE UNITS HISTOGRAM DISTANCE UPPER_WALLS | gridtools colvar bias function core adjmat generic setup |
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 COMBINE SUM FLUSH LESS_THAN DISTANCES DISTANCE UPPER_WALLS | multicolvar colvar function bias generic |
24.001 | hybrid Small Angle Scattering — hands-on guide | Federico Ballabio | Practical guide to the use of the hySAS module. | GYRATION SAXS PRINT STATS BIASVALUE ENSEMBLE RESTRAINT MOLINFO | isdb colvar bias function 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 | ||
22.017 | 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 | GROUP WHOLEMOLECULES PRINT EMMIVOX BIASVALUE MOLINFO | isdb core generic 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 | GROUP ENVIRONMENTSIMILARITY DUMPGRID SUM DISTANCE_MATRIX MATHEVAL MEAN CUSTOM Q6 UPPER_WALLS LOWER_WALLS MATRIX_VECTOR_PRODUCT HISTOGRAM OPES_METAD ONES MORE_THAN | matrixtools symfunc gridtools opes function bias envsim core adjmat generic |
21.005 | Replica exchange methods | Giovanni Bussi | Running umbrella sampling with replica exchange, bias exchange metadynamics and parallel tempering metadynamics | masterclass-2021 | METAD RANDOM_EXCHANGES PRINT RESTRAINT TORSION MOLINFO | generic colvar bias |
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 METAD TORSION INCLUDE DUMPFORCES PRINT | bias generic colvar |
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 | ||
24.015 | 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 LOAD DISTANCE | generic colvar 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 | METAD DISTANCE PATHMSD WHOLEMOLECULES PRINT MOVINGRESTRAINT CENTER UPPER_WALLS LOWER_WALLS MOLINFO | bias generic colvar vatom |
24.008 | Using the maze module | Jakub Rydzewski | Sampling ligand-protein dissociation using the maze module | protein, ligand, dissociation, unbinding, maze | CENTER DISTANCE GROUP COMMITTOR | vatom generic colvar core |
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 | UNITS METAD DISTANCE LOWER_WALLS BIASVALUE FLUSH UPPER_WALLS FIXEDATOM RESTART CUSTOM PRINT | vatom setup bias generic colvar function |
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 | ||
22.008 | 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 | MATRIX_VECTOR_PRODUCT ONES GROUP COORDINATIONNUMBER SUM PRINT DFSCLUSTERING MORE_THAN FLUSH MEAN RESTRAINT CLUSTER_DISTRIBUTION CLUSTER_NATOMS CONTACT_MATRIX | clusters matrixtools adjmat core bias generic function symfunc |
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 | PRINT PYTORCH_MODEL TORSION | generic colvar pytorch |
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_EXPLORE OPES_METAD TORSION ECV_MULTITHERMAL ECV_UMBRELLAS_LINE OPES_EXPANDED ENERGY | opes 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 | METAD DISTANCE GROUP WHOLEMOLECULES COMBINE RMSD EFFECTIVE_ENERGY_DRIFT DEBUG COORDINATION CUSTOM PRINT | core bias generic colvar function |
21.004 | Metadynamics | Max Bonomi | How to calculate statistical averages and free energy surfaces using metadynamics | masterclass-2021 | METAD DUMPGRID TORSION HISTOGRAM REWEIGHT_BIAS CONVERT_TO_FES PRINT MOLINFO | bias gridtools generic colvar |
21.003 | Umbrella Sampling | Giovanni Bussi | How to calculate statistical averages and free energy surfaces using umbrella sampling | masterclass-2021 | DUMPGRID TORSION PRINT HISTOGRAM BIASVALUE READ REWEIGHT_BIAS RESTRAINT CONVERT_TO_FES CUSTOM MOLINFO | bias gridtools generic colvar 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 | UNITS DUMPGRID DISTANCE METAD COORDINATIONNUMBER COM HISTOGRAM CONSTANT READ REWEIGHT_BIAS RESTRAINT UPPER_WALLS CUSTOM CONVERT_TO_FES AVERAGE PRINT | vatom setup bias gridtools generic colvar function symfunc |
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 | DISTANCE TORSION WHOLEMOLECULES COMBINE GYRATION ANTIBETARMSD CENTER PARABETARMSD ALPHARMSD DUMPATOMS PRINT MOLINFO | vatom secondarystructure generic colvar function |
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 | CUSTOM GYRATION UPPER_WALLS DISTANCE COORDINATIONNUMBER PRINT COM ONES COMBINE CONTACT_MATRIX MATRIX_VECTOR_PRODUCT MEAN COORDINATION LOWER_WALLS METAD FLUSH UNITS GROUP | setup bias adjmat symfunc generic function core matrixtools colvar vatom |
24.018 | Permutation Invariant Vector and Water Crystallisation | Silvio Pipolo, Fabio Pietrucci | Modelling water crystallisation using PIV variables | PIV, PathCV, Water Crystallisation | PIV FUNCPATHMSD UPPER_WALLS PRINT PLUMED CELL LOWER_WALLS METAD | bias piv generic function colvar |
24.010 | Modelling mechanobiological processes | Claire Pritchard, Guillaume Stirnemann and Glen Hocky | A tutorial on modelling mechanobiological processes | Metadynamics, pulling, force, rates, GPCR | DUMPATOMS BIASVALUE DISTANCE COMMITTOR PRINT COM METAD MATHEVAL UNITS RESTRAINT | setup bias generic function colvar vatom |
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 | RESTRAINT UPPER_WALLS DISTANCE PRINT TORSION RESTART COM EXTENDED_LAGRANGIAN COORDINATION LOWER_WALLS MOLINFO METAD FLUSH WHOLEMOLECULES UNITS GROUP | setup bias generic core colvar vatom |
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 READ COORDINATION METAD RESTRAINT FIT_TO_TEMPLATE UPPER_WALLS CONVERT_TO_FES ONES RMSD WHOLEMOLECULES GROUP KDE REWEIGHT_BIAS CUSTOM PRINT DUMPGRID ACCUMULATE WRAPAROUND FLUSH POSITION MATHEVAL HISTOGRAM | bias generic function core gridtools colvar vatom |
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 |
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 BIASVALUE TORSION PRINT PBMETAD MATHEVAL WHOLEMOLECULES | function colvar generic bias | |
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 BIASVALUE DISTANCE FISST PRINT METAD MATHEVAL UNITS RESTRAINT | setup bias generic fisst function 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 | ANTIBETARMSD GYRATION BIASVALUE LESS_THAN SASA_HASEL PRINT PARABETARMSD SUM SECONDARY_STRUCTURE_RMSD MOLINFO LOWEST ALPHARMSD | bias sasa generic secondarystructure function colvar |
22.011 | Variationally Enhanced Sampling | Omar Valsson | An introduction to running Variationally Enhanced Sampling (VES) using PLUMED. | masterclass-2022 Variationally Enhanced Sampling VES | OPT_AVERAGED_SGD REWEIGHT_BIAS UPPER_WALLS DISTANCE CONVERT_TO_FES PRINT TD_WELLTEMPERED BF_WAVELETS READ COORDINATION DUMPGRID TD_UNIFORM VES_LINEAR_EXPANSION HISTOGRAM BF_LEGENDRE | bias ves generic gridtools colvar |
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 |
22.009 | 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 DISTANCE PRINT LOWER_WALLS METAD UNITS | setup colvar generic bias |
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 | BIASVALUE DISTANCE PRINT TORSION MOLINFO MATHEVAL EDS | bias eds generic function colvar |
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 | ANTIBETARMSD PCA ALPHARMSD DUMPMULTICOLVAR RMSD PATH MORE_THAN UNITS GROUP LANDMARK_SELECT_FPS COORDINATIONNUMBER COMMITTOR TORSION PRINT SKETCHMAP PARABETARMSD PCAVARS DUMPVECTOR DUMPGRID DUMPPDB PROJECT_POINTS COLLECT_FRAMES FCCUBIC CLASSICAL_MDS MOLINFO HISTOGRAM | mapping setup dimred symfunc generic secondarystructure function landmarks core gridtools multicolvar 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 | GROUP GEOMETRIC_PATH VSTACK FIXEDATOM COORDINATIONNUMBER RDF SPHERICAL_HARMONIC ONES AVERAGE DUMPGRID GPATH GATHER_REPLICAS CONCATENATE LOCAL_AVERAGE BIASVALUE CUSTOM PRINT MATRIX_PRODUCT REFERENCE_GRID DFSCLUSTERING PDB2CONSTANT LOWEST WHOLEMOLECULES PATH INTEGRATE_GRID DISPLACEMENT COM VOLUME CONSTANT EUCLIDEAN_DISTANCE RMSD_VECTOR CLUSTER_WEIGHTS DOMAIN_DECOMPOSITION INTERPOLATE_GRID MEAN Q6 HISTOGRAM DISTANCE SORT Q1 DIFFERENCE RMSD SUM CONTACT_MATRIX DIAGONALIZE DISTANCES SELECT_COMPONENTS TRANSPOSE ACCUMULATE KDE SPRINT GSYMFUNC_THREEBODY TORSION MORE_THAN CLUSTER_PROPERTIES INSPHERE PCAVARS LESS_THAN OUTER_PRODUCT LOCAL_Q1 MATRIX_VECTOR_PRODUCT RESTRAINT POSITION COMBINE DISTANCE_MATRIX Q4 PAIRENTROPY CENTER | valtools multicolvar function matrixtools refdist colvar mapping generic bias clusters vatom adjmat sprint volumes gridtools symfunc core |