Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model

Victor Ovchinnikov, Simone Conti, Edmond Y. Lau, Felice C. Lightstone, Martin Karplus

Research output: Contribution to journalArticle

Abstract

We describe the development and implementation of a quasi-equilibrium hydration shell model of biomolecular solvation with adaptive boundaries. Applying the model to microsecond-long molecular dynamics simulations of several protein systems of varying complexity, we find that the model simulation results are of comparable quality to those obtained from simulations of fully solvated systems, but at a reduced computational cost. We discuss the dominant sources of error in the model and outline directions for future improvements.

Original languageEnglish (US)
Pages (from-to)1866-1881
Number of pages16
JournalJournal of Chemical Theory and Computation
Volume16
Issue number3
DOIs
StatePublished - Mar 10 2020
Externally publishedYes

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

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