Advances in Free-Energy Calculations Based on Classical Molecular Dynamics Simulations
Niels Hansen
- 01 Jan 2014
3
About: The article was published on 01 Jan 2014. and is currently open access. The article focuses on the topics: Molecular dynamics.
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Citations
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Efficient use of non-equilibrium measurement to estimate free energy differences for molecular systems
TL;DR: Two fully automated analyses of nonequilibrium data from a toy model, and various simulated molecular systems are presented, exploiting statistical properties of Jarzynski's equality to determine the best estimate for ΔF given a (finite) set of work values previously generated by simulation or experiment.
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•Journal Article
Charge Hydration Asymmetry: The Basic Principle and How to Use It to Test and Improve Water Models
TL;DR: In this paper, the rotational and charge inversion properties of a water molecule's charge distribution with its ability to cause charge hydration asymmetry are investigated. But the exact nature of this relationship is unknown.
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Molecular Theory Of Solutions
Monika Eisenhower
- 01 Jan 2016
TL;DR: The molecular theory of solutions is universally compatible with any devices to read and is available in the authors' digital library an online access to it is set as public so you can download it instantly.
References
Solubility of Organic Compounds in Water/Octanol Systems. A Expanded Ensemble Molecular Dynamics Simulation Study of log P Parameters
TL;DR: In this article, the expanded ensemble method was applied to calculate octanol/water partition coefficients P for some organic drug-related molecules and compared with experimental results, and the experimental log P results were obtained by a miniaturized vial procedure using liquid chromatography with UV for quantification.
66
Absolute Hydration Free Energies of Blocked Amino Acids: Implications for Protein Solvation and Stability
TL;DR: Molecular dynamics-based free energy simulations are used to calculate absolute hydration free energies for 15 N-acetyl-methylamide amino acids with neutral side chains and demonstrate that estimates of solvation free energies of full amino acids based on group-additive methods are systematically too negative and completely overestimate the hydrophobicity of glycine.
64
Relation between sequence similarity and structural similarity in proteins. Role of important properties of amino acids
TL;DR: The most important properties that determine the three-dimensional structure of a protein are conserved properties, i.e., are those that have been conserved during evolution, and bulk and hydrophobicity are more important than other properties, such as the preference for adopting a specific backbone structure.
64
On the Theory of Noncovalent Binding
TL;DR: A novel prediction of this approach, that expanding a ligand can increase its binding constant, is borne out by the simulations, and the simulations also show that abnormal binding isotherms can be obtained when the region over which the signal is detected deviates markedly from the exclusion zone.
63
Molecular Force Field Development for Aqueous Electrolytes: 1. Incorporating Appropriate Experimental Data and the Inadequacy of Simple Electrolyte Force Fields Based on Lennard-Jones and Point Charge Interactions with Lorentz-Berthelot Rules.
TL;DR: This paper describes a general parameter estimation methodology for a studied class of models that incorporates concentration-dependent experimental data for the total ionic chemical potential and the density into the fitting procedure, in addition to experimental values of solubility and solid chemical potential.
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