Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study. (Q38324310): Difference between revisions

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+A smooth particle mesh Ewald method
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reference URL: https://api.crossref.org/works/10.1016%2FS0301-4622%2899%2900007-1
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Revision as of 07:06, 10 July 2021

scientific article

Language	Label	Description	Also known as
English	Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study.	scientific article

Statements

scholarly article

1 reference

Europe PubMed Central

PubMed publication ID

2 September 2017

Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study. (English)

1 reference

Europe PubMed Central

PubMed publication ID

2 September 2017

J. Andrew McCammon

2

object named as

J A McCammon

1 reference

Europe PubMed Central

PubMed publication ID

2 September 2017

author name string

P H Hünenberger

1

1 reference

Europe PubMed Central

PubMed publication ID

2 September 2017

publication date

1 April 1999

1 reference

Europe PubMed Central

PubMed publication ID

2 September 2017

Biophysical Chemistry

1 reference

Europe PubMed Central

PubMed publication ID

2 September 2017

78

1 reference

Europe PubMed Central

PubMed publication ID

2 September 2017

1-2

1 reference

Europe PubMed Central

PubMed publication ID

2 September 2017

69-88

1 reference

Europe PubMed Central

PubMed publication ID

2 September 2017

Treatment of electrostatic effects in macromolecular modeling

1 reference

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7 January 2021

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Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects.

1 reference

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7 January 2021

based on heuristic

inferred from DOI database lookup

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

1 reference

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Consistent calculation of the static and frequency-dependent dielectric constant in computer simulations

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Effects of truncating long-range interactions in aqueous ionic solution simulations

1 reference

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Computer simulations do not support Cl-Cl pairing in aqueous NaCl solution

1 reference

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Cutoff size does strongly influence molecular dynamics results on solvated polypeptides

1 reference

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Molecular dynamics studies of solvated polypeptides: Why the cut-off scheme does not work

1 reference

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Taming cut-off induced artifacts in molecular dynamics studies of solvated polypeptides. The reaction field method.

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The effects of truncating long-range forces on protein dynamics.

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Computer simulation of aqueous Na-Cl electrolytes

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The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: how well is the X-ray structure "maintained"?

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Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution

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Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III).

1 reference

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A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions

1 reference

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A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation

1 reference

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7 January 2021

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RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin

1 reference

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7 January 2021

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Simulations of the molecular dynamics of nucleic acids

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Free Energy of Ionic Hydration

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Ion sizes and finite-size corrections for ionic-solvation free energies

1 reference

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7 January 2021

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Electrostatic interactions in periodic Coulomb and dipolar systems

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Correlations and free energies in restricted primitive model descriptions of electrolytes

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Effect of periodic box size on aqueous molecular dynamics simulation of a DNA dodecamer with particle-mesh Ewald method

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Gene cloning, expression, and characterization of the Sac7 proteins from the hyperthermophile Sulfolobus acidocaldarius.

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Solution Structure of the DNA-Binding Protein Sac7d from the Hyperthermophile Sulfolobus acidocaldarius

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Molecular dynamics simulations of the hyperthermophilic protein sac7d from Sulfolobus acidocaldarius: contribution of salt bridges to thermostability.

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A smooth particle mesh Ewald method

1 reference

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7 January 2021

based on heuristic

inferred from DOI database lookup

Identifiers

10.1016/S0301-4622(99)00007-1

1 reference

Europe PubMed Central

PubMed publication ID

2 September 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

2 September 2017

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