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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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
•Posted Content
Generalized-Ensemble Algorithms for Molecular Simulations of Biopolymers
TL;DR: In this paper, a review of the generalized ensemble algorithms for protein folding is presented, which combine the merits of the Monte Carlo and molecular dynamics versions of the algorithms. And three new generalized-ensemble algorithms are presented, including simulated tempering, replica exchange, and replica exchange.
37
Sampling of rare events using hidden restraints.
TL;DR: A method to enhance sampling of rare events makes use of distance or dihedral-angle restraints to overcome an energy barrier separating two metastable states or to stabilize a transition state between the two metastables states.
37
Determination of hydrocarbon-water partition coefficients from chromatographic data and based on solution thermodynamics and theory
TL;DR: In this paper, the octanol water and hexadecane-water partition coefficients for series of alkylbenzenes, alkanes, alkenes, alcohols, and bromoalkanes were determined by the generator column technique.
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A thermodynamic and solvatochromic investigation of the effect of water on the phase-transfer properties of octan-1-ol
Andrew J. Dallas,Peter W. Carr +1 more
TL;DR: The room temperature solubility of water in octan-1-ol is determined to be 2.5 mol dm −3, which is equivalent to a mole fraction of 0.29.
35
Asymmetric bias in free-energy perturbation measurements using two Hamiltonian-based models
Di Wu,David A. Kofke +1 more
TL;DR: It is shown that the bias in free-energy perturbation calculations is significantly smaller when sampling is performed on the system having a broader work distribution compared to the bias for FEP calculations that sample the system with a narrower distribution.
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