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 |