Practical aspects of free-energy calculations: a review

N Hansen, WF Van Gunsteren - Journal of chemical theory and …, 2014 - ACS Publications
Free-energy calculations in the framework of classical molecular dynamics simulations are
nowadays used in a wide range of research areas including solvation thermodynamics …

Recent advances in the continuous fractional component Monte Carlo methodology

A Rahbari, R Hens, M Ramdin, OA Moultos… - Molecular …, 2021 - Taylor & Francis
In this paper, we review recent advances in the Continuous Fractional Component Monte
Carlo (CFCMC) methodology and present a historic overview of the most important …

Dissipative particle dynamics: Systematic parametrization using water-octanol partition coefficients

RL Anderson, DJ Bray, AS Ferrante, MG Noro… - The Journal of …, 2017 - pubs.aip.org
We present a systematic, top-down, thermodynamic parametrization scheme for dissipative
particle dynamics (DPD) using water-octanol partition coefficients, supplemented by water …

The contribution of the ion–ion and ion–solvent interactions in a molecular thermodynamic treatment of electrolyte solutions

S Kournopoulos, MS Santos, S Ravipati… - The Journal of …, 2022 - ACS Publications
Develo** molecular equations of state to treat electrolyte solutions is challenging due to
the long-range nature of the Coulombic interactions. Seminal approaches commonly used …

A site density functional theory for water: Application to solvation of amino acid side chains

Y Liu, S Zhao, J Wu - Journal of chemical theory and computation, 2013 - ACS Publications
We report a site density functional theory (SDFT) based on the conventional atomistic
models of water and the universality ansatz of the bridge functional. The excess Helmholtz …

Partial atomic charges and their impact on the free energy of solvation

JPM Jämbeck, F Mocci, AP Lyubartsev… - Journal of …, 2013 - Wiley Online Library
Free energies of solvation (ΔG) in water and n‐octanol have been computed for common
drug molecules by molecular dynamics simulations with an additive fixed‐charge force field …

Dissolution of cellulose in room temperature ionic liquids: anion dependence

RS Payal, KK Bejagam, A Mondal… - The Journal of …, 2015 - ACS Publications
The dissolution of cellulosic biomass in room temperature ionic liquids (RTILs) is studied
through free energy calculations of its monomer, viz., cellobiose, within a molecular …

Performing solvation free energy calculations in LAMMPS using the decoupling approach

V Khanna, JI Monroe, MF Doherty, B Peters - Journal of Computer-Aided …, 2020 - Springer
The decoupling approach to solvation free energy calculations requires scaling the
interactions between the solute and the solution with all intramolecular interactions …

Predicting the solubility of solid phenanthrene: a combined molecular simulation and group contribution approach

AS Paluch, EJ Maginn - AIChE Journal, 2013 - Wiley Online Library
A simple correction to the infinite dilution activity coefficient computed via molecular
simulation for a nonelectrolyte solid solute in solution is proposed. The methodology adopts …

Small molecule solvation free energy: Enhanced conformational sampling using expanded ensemble molecular dynamics simulation

AS Paluch, DL Mobley, EJ Maginn - Journal of Chemical Theory …, 2011 - ACS Publications
We present an efficient expanded ensemble molecular dynamics method to calculate the
solvation free energy (or residual chemical potential) of small molecules with complex …