Constant pH coarse-grained molecular dynamics with stochastic charge neutralization

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Abstract

pH dependence abounds in biochemical systems; however, many simulation methods used to investigate these systems do not consider this property. Using a modified version of the hybrid non-equilibrium molecular dynamics (MD)/Monte Carlo algorithm, we include a stochastic charge neutralization method, which is particularly suited to the MARTINI force field and enables artifact-free Ewald summation methods in electrostatic calculations. We demonstrate the efficacy of this method by reproducing pH-dependent self-assembly and self-organization behavior previously reported in experimental literature. In addition, we have carried out experimental oleic acid titrations where we report the results in a more relevant way for the comparison with computational methods than has previously been done.
Original languageEnglish
Pages (from-to)4046−4051
Number of pages6
JournalJournal of Physical Chemistry Letters
Volume13
Issue number18
Early online date29 Apr 2022
DOIs
Publication statusPublished - 12 May 2022

Keywords

  • Constant pH
  • CpHMD
  • coarse grained molecular dynamics
  • particle mesh Ewald
  • Constant Charge
  • titration
  • Oleic acid
  • Fmoc
  • peptides
  • self-assembly

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