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, Bernard Pettitt

Research output: Contribution to journalArticle

11 Citations (Scopus)

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
Externally publishedYes

Fingerprint

alanine
Alanine
Integral equations
integral equations
Water
Molecular Dynamics Simulation
simulation
Peptides
Computer simulation
interactions
water
peptides
Molecular dynamics
Permittivity
permittivity
molecular dynamics

Keywords

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

ASJC Scopus subject areas

  • Biochemistry
  • Physical and Theoretical Chemistry
  • Biophysics

Cite this

Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation. / Prabhu, Ninad V.; Perkyns, John S.; Blatt, Herb D.; Smith, Paul E.; Pettitt, Bernard.

In: Biophysical Chemistry, Vol. 78, No. 1-2, 05.04.1999, p. 113-126.

Research output: Contribution to journalArticle

Prabhu, Ninad V. ; Perkyns, John S. ; Blatt, Herb D. ; Smith, Paul E. ; Pettitt, Bernard. / Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation. In: Biophysical Chemistry. 1999 ; Vol. 78, No. 1-2. pp. 113-126.
@article{88122a134c194c7e9d5a67899cd86357,
title = "Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation",
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.",
keywords = "Alanine, Integral equation, Molecular dynamics, PMF, Simulation, Solvent model, Stochastic dynamics",
author = "Prabhu, {Ninad V.} and Perkyns, {John S.} and Blatt, {Herb D.} and Smith, {Paul E.} and Bernard Pettitt",
year = "1999",
month = "4",
day = "5",
doi = "10.1016/S0301-4622(99)00014-9",
language = "English (US)",
volume = "78",
pages = "113--126",
journal = "Biophysical Chemistry",
issn = "0301-4622",
publisher = "Elsevier",
number = "1-2",

}

TY - JOUR

T1 - Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation

AU - Prabhu, Ninad V.

AU - Perkyns, John S.

AU - Blatt, Herb D.

AU - Smith, Paul E.

AU - Pettitt, Bernard

PY - 1999/4/5

Y1 - 1999/4/5

N2 - 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.

AB - 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.

KW - Alanine

KW - Integral equation

KW - Molecular dynamics

KW - PMF

KW - Simulation

KW - Solvent model

KW - Stochastic dynamics

UR - http://www.scopus.com/inward/record.url?scp=0033007965&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0033007965&partnerID=8YFLogxK

U2 - 10.1016/S0301-4622(99)00014-9

DO - 10.1016/S0301-4622(99)00014-9

M3 - Article

VL - 78

SP - 113

EP - 126

JO - Biophysical Chemistry

JF - Biophysical Chemistry

SN - 0301-4622

IS - 1-2

ER -