Conserve water: A method for the analysis of solvent in molecular dynamics

Matthew P. Harrigan, Diwakar Shukla, Vijay S. Pande

Research output: Contribution to journalArticlepeer-review

Abstract

Molecular dynamics with explicit solvent is favored for its ability to more correctly simulate aqueous biological processes and has become routine thanks to increasingly powerful computational resources. However, analysis techniques including Markov state models (MSMs) ignore solvent atoms and focus solely on solute coordinates despite solvent being implicated in myriad biological phenomena. We present a unified framework called "solvent-shells featurization" for including solvent degrees of freedom in analysis and show that this method produces better models. We apply this method to simulations of dewetting in the two-domain protein BphC to generate a predictive MSM and identify functional water molecules. Furthermore, the proposed methodology could be easily extended for building MSMs of any systems with indistinguishable components.

Original languageEnglish (US)
Pages (from-to)1094-1101
Number of pages8
JournalJournal of Chemical Theory and Computation
Volume11
Issue number3
DOIs
StatePublished - Mar 10 2015
Externally publishedYes

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

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