Analyzing and Biasing Simulations with PLUMED

Giovanni Bussi*, Gareth A. Tribello

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Abstract

This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of a collective variable and by then explaining how the free energy can be computed as a function of one or more collective variables. A number of practical issues mostly around periodic boundary conditions that arise when these types of calculations are performed using PLUMED are then discussed. Later parts of the chapter discuss how PLUMED can be used to perform enhanced sampling simulations that introduce simulation biases or multiple replicas of the system and Monte Carlo exchanges between these replicas. This section is then followed by a discussion on how free-energy surfaces and associated error bars can be extracted from such simulations by using weighted histogram and block averaging techniques.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.,U.S.
Pages529-578
Number of pages50
DOIs
Publication statusPublished - 01 Jan 2019

Publication series

NameMethods in Molecular Biology
Volume2022
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • Collective variables
  • Enhanced sampling
  • Free energy
  • PLUMED
  • Replica exchange
  • WHAM

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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