Low-mass molecular dynamics simulation for configurational sampling enhancement: More evidence and theoretical explanation

Research output: Contribution to journalArticle

7 Scopus citations

Abstract

It has been reported recently that classical, isothermal-isobaric molecular dynamics (NTP MD) simulations at a time step of 1.00fs of the standard-mass time (δt=1.00fs<sup>smt</sup>) and a temperature of ≤340K using uniformly reduced atomic masses by tenfold offers better configurational sampling than standard-mass NTP MD simulations at the same time step. However, it has long been reported that atomic masses can also be increased to improve configurational sampling because higher atomic masses permit the use of a longer time step. It is worth investigating whether standard-mass NTP MD simulations at δt=2.00 or 3.16fs<sup>smt</sup> can offer better or comparable configurational sampling than low-mass NTP MD simulations at δt=1.00fs<sup>smt</sup>. This article reports folding simulations of two β-hairpins showing that the configurational sampling efficiency of NTP MD simulations using atomic masses uniformly reduced by tenfold at δt=1.00fs<sup>smt</sup> is statistically equivalent to and better than those using standard masses at δt=3.16 and 2.00fs<sup>smt</sup>, respectively. The results confirm that, relative to those using standard masses at routine δt=2.00fs<sup>smt</sup>, the low-mass NTP MD simulations at δt=1.00fs<sup>smt</sup> are a simple and generic technique to enhance configurational sampling at temperatures of ≤340K.

Original languageEnglish (US)
Article number79
Pages (from-to)126-133
Number of pages8
JournalBiochemistry and Biophysics Reports
Volume4
DOIs
StatePublished - Dec 1 2015

Keywords

  • Chignolin
  • CLN025
  • Folding rate
  • Folding time
  • Molecular dynamics simulation
  • Protein folding

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Cell Biology
  • Molecular Biology

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