Isokinetic approach in logarithmic mean-force dynamics for on-the-fly free energy reconstruction

Tetsuya Morishita, Takenobu Nakamura, Wataru Shinoda, Atsushi M. Ito

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)

Abstract

Logarithmic mean-force dynamics (LogMFD) is one of free energy calculation methods that utilize fictitious dynamical variables for efficient conformational sampling. In this study, we extend the LogMFD method to incorporate the isokinetic dynamics for the fictitious dynamical variables. The isokinetic LogMFD approach requires no additional parameter for thermostatting and it obviates the issue associated with the dynamics of the thermostat variable in Nosé-Hoover type thermostats. These virtues therefore make it easier to set up and undertake LogMFD calculations. The validity of the isokinetic algorithm introduced in LogMFD is examined by a benchmark system of alanine dipeptide in explicit water.

Original languageEnglish
Pages (from-to)633-640
Number of pages8
JournalChemical Physics Letters
Volume706
DOIs
Publication statusPublished - Aug 16 2018
Externally publishedYes

Keywords

  • Free energy
  • Isokinetic dynamics
  • Logarithmic mean-force dynamics
  • Molecular dynamics
  • Protein conformational change
  • Protein structure
  • Thermostat

ASJC Scopus subject areas

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

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