Constrained molecular dynamics in the isothermal-isobaric ensemble and its adaptation for adiabatic free energy dynamics

T. Q. Yu, Mark Tuckerman

Research output: Contribution to journalArticle

Abstract

The implementation of holonomic constraints within measure-preserving integrators for molecular dynamics simulations in the isothermal-isobaric ensemble is considered. We review the basic methodology of generating measure-preserving integrators for the microcanonical, canonical, and isothermal-isobaric ensembles and proceed to show how the standard SHAKE and RATTLE algorithms must be modified for the isothermal-isobaric ensemble. Comparison is made between constrained and unconstrained simulations employing multiple time scale integration techniques. Finally, we describe a temperature accelerated version of the isothermal-isobaric molecular dynamics approach, in which the cell matrix is adiabatically decoupled from the particles and maintained at a high temperature as a means of exploring polymorphism in molecular crystals. We demonstrate that constraints can be easily adapted for this new approach and, again, we compare the performace of this temperature-accelerated scheme with and without bond constraints.

Original languageEnglish (US)
Pages (from-to)183-209
Number of pages27
JournalEuropean Physical Journal: Special Topics
Volume200
Issue number1
DOIs
StatePublished - Nov 2011

Fingerprint

Free energy
Molecular dynamics
free energy
integrators
molecular dynamics
preserving
Molecular crystals
polymorphism
Polymorphism
Temperature
simulation
methodology
temperature
Computer simulation
matrices
cells
crystals

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Materials Science(all)
  • Physical and Theoretical Chemistry

Cite this

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abstract = "The implementation of holonomic constraints within measure-preserving integrators for molecular dynamics simulations in the isothermal-isobaric ensemble is considered. We review the basic methodology of generating measure-preserving integrators for the microcanonical, canonical, and isothermal-isobaric ensembles and proceed to show how the standard SHAKE and RATTLE algorithms must be modified for the isothermal-isobaric ensemble. Comparison is made between constrained and unconstrained simulations employing multiple time scale integration techniques. Finally, we describe a temperature accelerated version of the isothermal-isobaric molecular dynamics approach, in which the cell matrix is adiabatically decoupled from the particles and maintained at a high temperature as a means of exploring polymorphism in molecular crystals. We demonstrate that constraints can be easily adapted for this new approach and, again, we compare the performace of this temperature-accelerated scheme with and without bond constraints.",
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