Peptides in ionic solutions: A comparison of the Ewald and switching function techniques

Paul E. Smith, Bernard Pettitt

Research output: Contribution to journalArticle

153 Citations (Scopus)

Abstract

The methodological dependence of observed ion-peptide associations in molecular dynamics simulations is investigated. We compare the results from several simulations of a pentapeptide in explicit solvent and salt ions which differ in the their treatment of the long ranged electrostatic interactions. Results for both the Ewald and switching function techniques are presented. It was found that there were important differences between the two methods for the water dipole-dipole temporal and spatial correlations, total dipole moment fluctuations, and self-diffusion constants. Electrostatic potentials calculated in the region of the peptide are also used to illustrate the large differences that can arise from different treatments of the electrostatic interactions. It appears that the switching function distorts the molecular electrostatic potential experienced by the salt ions to such a degree that their behaviour becomes highly dependent on the initial conditions. In summary, the use of a switching function is not recommended for the simulation of ions and their interactions with biomolecules.

Original languageEnglish (US)
Pages (from-to)8430-8441
Number of pages12
JournalJournal of Chemical Physics
Volume95
Issue number11
StatePublished - 1991
Externally publishedYes

Fingerprint

Switching functions
peptides
Ions
electrostatics
Peptides
Coulomb interactions
Electrostatics
ions
Salts
dipoles
salts
simulation
Dipole moment
interactions
Biomolecules
Molecular dynamics
dipole moments
molecular dynamics
Water
Computer simulation

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

Peptides in ionic solutions : A comparison of the Ewald and switching function techniques. / Smith, Paul E.; Pettitt, Bernard.

In: Journal of Chemical Physics, Vol. 95, No. 11, 1991, p. 8430-8441.

Research output: Contribution to journalArticle

@article{b2e8fe89ec9c4625b523d5e1d03f9f85,
title = "Peptides in ionic solutions: A comparison of the Ewald and switching function techniques",
abstract = "The methodological dependence of observed ion-peptide associations in molecular dynamics simulations is investigated. We compare the results from several simulations of a pentapeptide in explicit solvent and salt ions which differ in the their treatment of the long ranged electrostatic interactions. Results for both the Ewald and switching function techniques are presented. It was found that there were important differences between the two methods for the water dipole-dipole temporal and spatial correlations, total dipole moment fluctuations, and self-diffusion constants. Electrostatic potentials calculated in the region of the peptide are also used to illustrate the large differences that can arise from different treatments of the electrostatic interactions. It appears that the switching function distorts the molecular electrostatic potential experienced by the salt ions to such a degree that their behaviour becomes highly dependent on the initial conditions. In summary, the use of a switching function is not recommended for the simulation of ions and their interactions with biomolecules.",
author = "Smith, {Paul E.} and Bernard Pettitt",
year = "1991",
language = "English (US)",
volume = "95",
pages = "8430--8441",
journal = "Journal of Chemical Physics",
issn = "0021-9606",
publisher = "American Institute of Physics Publising LLC",
number = "11",

}

TY - JOUR

T1 - Peptides in ionic solutions

T2 - A comparison of the Ewald and switching function techniques

AU - Smith, Paul E.

AU - Pettitt, Bernard

PY - 1991

Y1 - 1991

N2 - The methodological dependence of observed ion-peptide associations in molecular dynamics simulations is investigated. We compare the results from several simulations of a pentapeptide in explicit solvent and salt ions which differ in the their treatment of the long ranged electrostatic interactions. Results for both the Ewald and switching function techniques are presented. It was found that there were important differences between the two methods for the water dipole-dipole temporal and spatial correlations, total dipole moment fluctuations, and self-diffusion constants. Electrostatic potentials calculated in the region of the peptide are also used to illustrate the large differences that can arise from different treatments of the electrostatic interactions. It appears that the switching function distorts the molecular electrostatic potential experienced by the salt ions to such a degree that their behaviour becomes highly dependent on the initial conditions. In summary, the use of a switching function is not recommended for the simulation of ions and their interactions with biomolecules.

AB - The methodological dependence of observed ion-peptide associations in molecular dynamics simulations is investigated. We compare the results from several simulations of a pentapeptide in explicit solvent and salt ions which differ in the their treatment of the long ranged electrostatic interactions. Results for both the Ewald and switching function techniques are presented. It was found that there were important differences between the two methods for the water dipole-dipole temporal and spatial correlations, total dipole moment fluctuations, and self-diffusion constants. Electrostatic potentials calculated in the region of the peptide are also used to illustrate the large differences that can arise from different treatments of the electrostatic interactions. It appears that the switching function distorts the molecular electrostatic potential experienced by the salt ions to such a degree that their behaviour becomes highly dependent on the initial conditions. In summary, the use of a switching function is not recommended for the simulation of ions and their interactions with biomolecules.

UR - http://www.scopus.com/inward/record.url?scp=26744435700&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=26744435700&partnerID=8YFLogxK

M3 - Article

AN - SCOPUS:26744435700

VL - 95

SP - 8430

EP - 8441

JO - Journal of Chemical Physics

JF - Journal of Chemical Physics

SN - 0021-9606

IS - 11

ER -