Constant-pH molecular dynamics using stochastic titration

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Abstract

The constant-pH molecular dynamics (MD) simulations were performed using the stochastic titration. The protonation state of each titrable site in the solute was allowed to change during a molecular mechanics (MM) simulations. The stochastic titration method was applied to succinic acid for illustrating the method and examining the choice of its adjustable parameters. The most critical parameter of the method was the time given to the solvent to relax after each protonation change.

Original languageEnglish
Pages (from-to)4184-4200
Number of pages17
JournalJournal of Chemical Physics
Volume117
Issue number9
DOIs
Publication statusPublished - 1 Sep 2002

Keywords

  • Proteins
  • Titration
  • Algorithms
  • Binding energy
  • Computer simulation
  • Continuum mechanics
  • Dissociation
  • Electrostatics
  • Entropy
  • Free energy
  • Hamiltonians
  • Isomerization
  • Monte Carlo methods
  • Parameter estimation
  • pH effects
  • Protons

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