An assessment of potential of mean force calculations with implicit solvent models

Article Abstract:

A series of molecular dynamics simulations on a small peptide are used to assess the ability of different solvent models to reproduce experimental data using different implicit solvent models. The results revealed that all simulations, which employed an implicit solvent model yielded values for the fluorescent resonance energy transfer (FRET) that significantly deviated from the experimental value.

Electric properties, Energy transfer

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Characterization of hydrogen bonding in a continuum solvent model

Article Abstract:

A simple approach for calculating hydrogen bonding (H-bonding) effects in molecular mechanics simulations of peptides and proteins is presented for use in the framework of the continuum solvent model. The H-bonding description is easily implemented in standard force fields, with virtually no additional computing time requirements.

Proteins, Hydrogen bonding, Properties

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A general treatment of solvent effects based on screened coulomb potentials

Article Abstract:

A new implicit solvent model for Monte Carlo simulations of peptides and proteins is presented. A new formulation of an implicit solvent model is proposed based on screened Coulomb potentials.

Usage, Monte Carlo method, Monte Carlo methods

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