Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation

Ninad V. Prabhu, John S. Perkyns, Herb D. Blatt, Paul E. Smith, B. Montgomery Pettitt

Research output: Contribution to journalArticle

11 Scopus citations

Abstract

The dielectrically consistent reference interaction site model (DRISM) integral equation theory is applied to determine the potential of mean force (PMF) for an alanine tetramer. A stochastic dynamics simulation of the alanine tetramer using this PMF is then compared with an explicit water molecular dynamics simulation. In addition, comparison is also done with simulations using other solvent models like the extended reference interaction site model (XRISM) theory, constant dielectric and linear distance-dependent dielectric models. The results show that the DRISM method offers a fairly accurate and computationally inexpensive alternative to explicit water simulations for studies on small peptides. Copyright (C) 1999 Elsevier Science B.V. All rights reserved.

Original languageEnglish (US)
Pages (from-to)113-126
Number of pages14
JournalBiophysical Chemistry
Volume78
Issue number1-2
DOIs
StatePublished - Apr 5 1999

Keywords

  • Alanine
  • Integral equation
  • Molecular dynamics
  • PMF
  • Simulation
  • Solvent model
  • Stochastic dynamics

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Organic Chemistry

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