ASE-PLUMED Tutorial

A tutorial about the ASE-PLUMED calculator presented in Sucerquia et. al., JCP, 2022 [1]

by Daniel Sucerquia, Pilar Cossio and Olga Lopez-Acevedo.

This tutorial shows how to use the plumed calculator in ASE.

The Atomic Simulation Environment, ASE, is a package that allows setting up, run and visualize atomistic simulations. It is interfaced with some other codes, which use quantum or classical methods. We developed a plumed calculator to connect PLUMED with all the other codes interfaced in ASE. We note that PLUMED allows several actions in addition of what we show in this tutorial. For further description, visit plumed web page.

This tutorial begins with a brief explanation of the basic ideas about metadynamics. We first use a toy model to show how to compute collective variables on-the-fly in an MD simulation, and also from a previously computed MD trajectory using post-processing. We then implement Well-Tempered Metadynamics to reconstruct the free energy surface of the toy system along a set of collective variables. Finally, we present a more realistic example for a small silver cluster that uses ab-initio metadynamics to estimate the free energy landscape. All the files required to complete this tutorial are publicly available in https://github.com/Sucerquia/ASE-PLUMED_tutorial/blob/master/files.

[1] Sucerquia, Daniel, Cristian Parra, Pilar Cossio, and Olga Lopez-Acevedo. “Ab Initio Metadynamics Determination of Temperature-Dependent Free-Energy Landscape in Ultrasmall Silver Clusters.” The Journal of Chemical Physics 156, no. 15 (April 21, 2022): 154301. https://doi.org/10.1063/5.0082332

flowchart TB;
  Z[PLUMED syntax] -.-> A[ASE-PLUMED tutorial]
  A -.-> B[Install packages]
  A ==> C[Theory: CVs and MTD]
  A ==> D[Toy model: Planar 7-Atoms Cluster]
  D ==> E[Unbiased simulation and Postprocessing]
  D ==> F[Biased simulation: Well Tempered Metadynamics]
  F -.-> G[Restart a simulation]
  A ==> H[Ab-initio: Small Silver Cluster]

  click Z "../../../21/001/data/NAVIGATION.html" "A previous tutorial that introduces the basics of PLUMED syntax"
  click B "install.html" "Install py-plumed and ASE"
  click C "theory.html" "Theory necessary to follow completely this tutorial"
  click D "defsystem.html" "Toy model showing the usage of PLUMED in ASE"
  click E "MD.html" "Unbiased simulation computing CVs on the fly and by postprocessing"
  click F "MTD.html" "Addition of the bias using metadynamics"
  click G "restart.html" "How to restart a simulation in ASE"
  click H "SC.html" "Ab-initio example"

Theory: CVs and MTD →

Click here to open manual pages for actions discussed in this tutorial.