Tutorials

The following pages describe how to perform a variety of tasks using PLUMED

Trieste tutorial: Analyzing trajectories using PLUMED This tutorial explains how to use PLUMED to analyze trajectories
Trieste tutorial: Averaging, histograms and block analysis Averaging, histograms and block averaging
Trieste tutorial: Using restraints This tutorial explains how to use PLUMED to run simple restrained simulations and account for the bias in the analysis
Trieste tutorial: Metadynamics simulations with PLUMED This tutorial explains how to use PLUMED to run metadynamics simulations
Trieste tutorial: Running and analyzing multi-replica simulations. This tutorial explains how to use PLUMED to run and analyze multi-replica simulations
Trieste tutorial: Real-life applications with complex CVs 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
Master ISDD tutorial: 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: Metadynamics simulations with PLUMED This tutorial explains how to use PLUMED to run metadynamics simulations
Belfast tutorial: Analyzing CVs This tutorial explains how to use plumed to analyze CVs
Belfast tutorial: Adaptive variables I How to use path CVs
Belfast tutorial: Adaptive variables II Dimensionality reduction and sketch maps
Belfast tutorial: Umbrella sampling Umbrella sampling, reweighting, and weighted histogram
Belfast tutorial: Out of equilibrium dynamics How to run a steered MD simulations and how to estimate the free energy
Belfast tutorial: Metadynamics How to run a metadynamics simulation
Belfast tutorial: Replica exchange I Parallel tempering and Metadynamics, Well-Tempered Ensemble
Belfast tutorial: Replica exchange II and Multiple walkers Bias exchange and multiple walkers
Belfast tutorial: NMR restraints NMR restraints
Belfast tutorial: Steinhardt Parameters Steinhardt Parameters
Cambridge tutorial A short 2 hours tutorial that introduces Well-Tempered Metadynamics, Bias-Exchange Metadynamics and Replica-Average Metadynamics
CINECA tutorial A short 2 hours tutorial that introduces analysis, well-tempered metadynamics, and multiple-restraints umbrella sampling.
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
Moving from PLUMED 1 to PLUMED 2 This tutorial explains how plumed 1 input files can be translated into the new plumed 2 syntax.
Munster tutorial A short 3 hours tutorial that introduces analysis, well-tempered metadynamics, and multiple-restraints umbrella sampling.
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