 |
 |
 |
| |
|
|
The following pages describe how to perform a variety of tasks using PLUMED
| Master ISDD tutorial 2024: Brief introduction to PLUMED | This tutorial explains the syntax of the PLUMED input file and how to use PLUMED to analyze CVs |
| Master ISDD tutorial 2024: Metadynamics simulations with PLUMED | This tutorial explains how to use PLUMED to run metadynamics simulations |
| PLUMED Masterclass 22.1: Funnel-Metadynamics | This Masterclass explains how to use PLUMED to run and analyze Funnel-Metadynamics simulations |
| PLUMED Masterclass 22.2: Analysis of Plumed output by Metadynminer | This Masterclass explains the use of R package Metadynminer to analyze metadynamics results. |
| PLUMED Masterclass 22.3: OPES method | This Masterclass shows how to use PLUMED to run and analyze OPES simulations |
| PLUMED Masterclass 22.5: Machine learning collective variables with Pytorch | This Masterclass shows how to train machine learning-based CVs in PyTorch and deploy them in PLUMED. |
| PLUMED Masterclass 22.6: EDS module + Coarse-Grained directed simulations | This Masterclass describes how to bias simulations to agree with experimental data using experiment directed simulation. |
| PLUMED Masterclass 22.8: Modelling Concentration-driven processes with PLUMED | This Masterclass discusses the analysis and simulation of processes driven by concentration such as nucleation, diffusion and growth with PLUMED. |
| PLUMED Masterclass 22.9: Using path collective variables to find reaction mechanisms in complex free energy landscapes | This Masterclass explains the syntax of the PLUMED input file and how to use PLUMED to analyze CVs |
| PLUMED Masterclass 22.10: Hamiltonian replica exchange with PLUMED and GROMACS | This Masterclass explains how to use Hamiltonian replica exchange simulations with GROMACS + PLUMED |
| PLUMED Masterclass 22.11: Variationally enhanced sampling with PLUMED | This Masterclass explains how to run variationally enhanced sampling simulations with PLUMED |
| PLUMED Masterclass 22.12: Liquid-solid chemical potential differences with the environment similarity CV | This Masterclass explains how to compute chemical potential differences between the liquid and a solid with the environment similarity CV |
| PLUMED Masterclass 22.13: SASA module and the application of PLUMED for implicit solvent simulations | This Masterclass explains how to use the SASA module of PLUMED to perform implicit solvent simulations |
| PLUMED Masterclass 22.15: FISST module and application of mechanical forces with PLUMED | This Masterclass explains how to use the SASA module of PLUMED to perform implicit solvent simulations |
| PLUMED Masterclass 21.1: PLUMED syntax and analysis | This Masterclass explains the syntax of the PLUMED input file and how to use PLUMED to analyze CVs |
| PLUMED Masterclass 21.2: Statistical errors in MD | This Masterclass explains how to report averages, histograms and the associated error bars so that others can reproduce your results. |
| PLUMED Masterclass 21.3: Umbrella sampling | This Masterclass explains how to use PLUMED to run simple restrained simulations and account for the bias in the analysis |
| PLUMED Masterclass 21.4: Metadynamics | This Masterclass explains how to use PLUMED to run and analyze metadynamics simulations |
| PLUMED Masterclass 21.5: Simulations with multiple replicas | This Masterclass explains how to use PLUMED to run multiple-replica simulations |
| PLUMED Masterclass 21.6: Dimensionality reduction | This Masterclass explains how to select collective variables in a variety of contexts |
| PLUMED Masterclass 21.7: Optimizing PLUMED performances | This Masterclass explains how to use optimize PLUMED performances |
| Advanced Methods in MD 2023: Metadynamics simulations with PLUMED | This tutorial explains how to use PLUMED to run metadynamics simulations |
| Lugano tutorial: Brief guide to PLUMED syntax and analyzing trajectories | This tutorial explains the syntax of the PLUMED input file and how to use PLUMED to analyze CVs |
| Lugano tutorial: Using restraints | This tutorial explains how to use PLUMED to run simple restrained simulations and account for the bias in the analysis |
| Lugano tutorial: Metadynamics simulations with PLUMED | This tutorial explains how to use PLUMED to run metadynamics simulations |
| Lugano tutorial: Calculating error bars | Calculating error bars |
| Lugano tutorial: Dimensionality reduction | How to perform dimensionality reduction using PLUMED |
| Lugano tutorial: Using PLUMED with LAMMPS | An exercise on running PLUMED with LAMMPS |
| Lugano tutorial: Binding of a ion and a dinucleotide | An exercise to compute binding free energies |
| Lugano tutorial: Computing proton transfer in water | An exercise to run a simple proton transfer calculation with CP2K |
| Lugano tutorial: Folding free energy for a protein described by a go-model | This tutorial propose a more complex case to test your own skill with a more realistic example |
| Using Hamiltonian replica exchange with GROMACS | This tutorial explains how to use Hamiltonian replica exchange in GROMACS |
| Julich tutorial: Developing CVs in plumed | Implementing new collective variables in plumed |
| ESDW Workshop Lyon 2019: A very simple introduction to PLUMED | This tutorial gives a brief introduction to PLUMED by showing how it can be used to study a cluster of 7 Lennard Jones atoms. |
| MARVEL tutorial: Analyzing CVs | This tutorial explains how to use PLUMED to analyze CVs |
| MARVEL tutorial: Path CVs | This tutorial explains how to use various kinds of path collective variables |
| new-munster | This tutorial explains how to use PLUMED to run metadynamics simulations |
| Optimizing PLUMED performance | A short 1.5 hours tutorial that introduces performance optimization |
In addition, the following websites contain resources that might be helpful
| http://www.youtube.com/watch?v=iDvZmbWE5ps | A short video introduction to the use of multicolvars in PLUMED 2 |
| http://www.youtube.com/watch?v=PxJP16qNCYs | A short video introduction to the syntax of the PLUMED 2 input file |
| http://en.wikipedia.org/wiki/Metadynamics | A wikipedia article on metadynamics |
Some older tutorials are also available here (some of them cover topics not covered by the recent tutorial but syntax may be outdated):
1.8.17