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
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TL;DR: A polarizable potential model for M(+)-NH3 interactions is optimized based on the ab initio properties of the ion-ammonia dimers and gives relative solvation free energies in liquid ammonia in good agreement with experimental data, without further adjustments.
Computing the relative stabilities and the per-residue components in protein conformational changes.
TL;DR: It is shown how the total conversion free energies can be parsed into per-residue free-energy components, which opens up the possibility for systematic improvements in structure-prediction scoring functions, in the design of protein conformational switches, and in interpreting protein mechanisms at the amino-acid level.
Fluctuation-based computer calculation of partial molar properties. II. A numerically accurate method for the determination of partial molar energies and enthalpies
TL;DR: In this paper, a new operational definition of the partial molar energy is derived invoking the grand canonical ensemble formalism, used in conjunction with the fluctuation-explicit form of the Kirkwood-Buff relation for partial molars volumes, allowing the accurate computer calculation of all mechanical partialmolar properties in a multicomponent system.
Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations
TL;DR: The results of this test reveal that the force field parameters for some groups of molecules (such as hydroxyl-rich compounds) still need to be improved, but for most compounds, accuracy was consistent with that seen in the previous tests.
Predictions of Hydration Free Energies from All-Atom Molecular Dynamics Simulations†
TL;DR: The aqueous solvation free energies of 52 small drug-like molecules using an all-atom force field in explicit water are computed using several different charge models and it is found that hypervalent sulfur and phosphorus compounds are not well handled using current force field parameters.