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

doi:10.1016/S0301-4622(99)00014-9

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 journal › Article › peer-review

12 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 language	English (US)
Pages (from-to)	113-126
Number of pages	14
Journal	Biophysical Chemistry
Volume	78
Issue number	1-2
DOIs	https://doi.org/10.1016/S0301-4622(99)00014-9
State	Published - Apr 5 1999
Externally published	Yes

Keywords

Alanine
Integral equation
Molecular dynamics
PMF
Simulation
Solvent model
Stochastic dynamics

ASJC Scopus subject areas

Biophysics
Biochemistry
Organic Chemistry

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10.1016/S0301-4622(99)00014-9

Cite this

@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 Pettitt, {B. Montgomery}",

note = "Funding Information: The authors thank the N.I.H. and Robert A. Welch Foundation for partial support. HDB was supported by a fellowship from the Keck Center for Computational Biology and the NSF. Molecular Simulations, Inc. is thanked for visualization software. Dr Gillian Lynch and Michael Feig are thanked for stimulating discussion. ",

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doi = "10.1016/S0301-4622(99)00014-9",

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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, B. Montgomery

N1 - Funding Information: The authors thank the N.I.H. and Robert A. Welch Foundation for partial support. HDB was supported by a fellowship from the Keck Center for Computational Biology and the NSF. Molecular Simulations, Inc. is thanked for visualization software. Dr Gillian Lynch and Michael Feig are thanked for stimulating discussion.

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

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AN - SCOPUS:0033007965

SN - 0301-4622

VL - 78

SP - 113

EP - 126

JO - Biophysical Chemistry

JF - Biophysical Chemistry

IS - 1-2

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

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