Journal ArticleDOI
Free energy calculations for Lennard-Jones systems and water using the expanded ensemble method A Monte Carlo and molecular dynamics simulation study
TLDR
In this paper, the free energy for simple point charge water (rigid and flexible) is calculated using the Lennard-Jones system as a reference and the results are in accordance with results obtained using other methods for calculation of free energy in computer simulations.Abstract:
The method of expanded ensembles for calculation of free energy in Monte Carlo simulations is incorporated into molecular dynamics simulations. Calculations of the free energy for the Lennard-Jones system are carried out using both variants of the expanded ensemble method (i.e. Monte Carlo and molecular dynamics simulations) and are shown to give identical results. The free energy for two variants of the simple point charge water (rigid and flexible) is calculated using the Lennard-Jones system as a reference. Numerically very accurate results for the free energy are obtained. The results are in accordance with results obtained using other methods for calculation of free energy in computer simulations. The advantages of the presented method and possible applications for calculation of free energies for more complicated molecular systems are discussed.read more
Citations
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Guidelines for the analysis of free energy calculations
TL;DR: This work reviews and recommends best practices for analysis yielding reliable free energies from molecular simulations, and provides a Python tool, alchemical-analysis.py, that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages.
Journal ArticleDOI
ms2: A Molecular Simulation Tool for Thermodynamic Properties
Stephan Deublein,Bernhard Eckl,Jürgen Stoll,Sergey V. Lishchuk,Gabriela Guevara-Carrion,Colin W. Glass,Thorsten Merker,Martin Bernreuther,Hans Hasse,Jadran Vrabec +9 more
TL;DR: This work presents the molecular simulation programms2 that is designed for the calculation of thermodynamic properties of bulk fluids in equilibrium consisting of small electro-neutral molecules, written in Fortran90 and optimized for a fast execution on a broad range of computer architectures.
Journal ArticleDOI
A method for computing the solubility limit of solids: Application to sodium chloride in water and alcohols
TL;DR: An adaptable method to compute the solubility limit of solids by molecular simulation, which avoids the difficulty of reference state calculations and is highly adaptable to molecules of complex topology is presented.
Journal ArticleDOI
Grand canonical ensemble molecular dynamics simulations: Reformulation of extended system dynamics approaches
TL;DR: In this paper, the extended system Hamiltonian for carrying out grand canonical ensemble molecular dynamics simulations is reformulated, including a generalized treatment of the reference state partition function of the total chemical potential that reproduces the ideal gas behavior.
Journal ArticleDOI
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.
References
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Journal ArticleDOI
A molecular dynamics method for simulations in the canonical ensemble
TL;DR: In this paper, a molecular dynamics simulation method which can generate configurations belonging to the canonical (T, V, N) ensemble or the constant temperature constant pressure ensemble was proposed, which is tested for an atomic fluid (Ar) and works well.
Journal ArticleDOI
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
G.M. Torrie,John P. Valleau +1 more
TL;DR: In this paper, the authors describe the use of arbitrary sampling distributions chosen to facilitate the estimate of the free energy difference between a model system and some reference system, but the conventional Monte Carlo methods of obtaining such averages are inadequate for the free-energy case.
Journal ArticleDOI
Some Topics in the Theory of Fluids
TL;DR: In this article, it was shown how certain thermodynamic functions, and also the radial distribution function, can be expressed in terms of the potential energy distribution in a fluid and a miscellany of results were derived from this unified point of view.
Journal ArticleDOI
Efficient estimation of free energy differences from Monte Carlo data
TL;DR: Near-optimal strategies are developed for estimating the free energy difference between two canonical ensembles, given a Metropolis-type Monte Carlo program for sampling each one, and their efficiency is never less or greater than that obtained by sampling only one ensemble.
Journal ArticleDOI
The Lennard-Jones equation of state revisited
TL;DR: In this paper, a modified Benedict-Webb-Rubin (MBWR) equation of state for the Lennard-Jones (LJ) fluid is presented and compared with the simulation data of this work, and previously published Gibbs ensemble data.