Recent force field strategies for intrinsically disordered proteins

J Mu, H Liu, J Zhang, R Luo… - Journal of chemical …, 2021 - ACS Publications
Intrinsically disordered proteins (IDPs) are widely distributed across eukaryotic cells, playing
important roles in molecular recognition, molecular assembly, post-translational …

Recent applications of Kirkwood–Buff theory to biological systems

V Pierce, M Kang, M Aburi, S Weerasinghe… - Cell biochemistry and …, 2008 - Springer
The effect of cosolvents on biomolecular equilibria has traditionally been rationalized using
simple binding models. More recently, a renewed interest in the use of Kirkwood–Buff (KB) …

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force‐field parameter sets 53A5 and 53A6

C Oostenbrink, A Villa, AE Mark… - Journal of …, 2004 - Wiley Online Library
Successive parameterizations of the GROMOS force field have been used successfully to
simulate biomolecular systems over a long period of time. The continuing expansion of …

Convergence of sampling Kirkwood–Buff integrals of aqueous solutions with molecular dynamics simulations

P Ganguly, NFA van der Vegt - Journal of chemical theory and …, 2013 - ACS Publications
We discuss two methods for calculating Kirkwood–Buff integrals (KBIs) of aqueous cosolvent
solutions from molecular simulations. The first method is based on computing running …

A Kirkwood–Buff derived force field for sodium chloride in water

S Weerasinghe, PE Smith - The Journal of chemical physics, 2003 - pubs.aip.org
A force field for the simulation of mixtures of sodium chloride and water is described. The
model is specifically designed to reproduce the experimentally determined Kirkwood–Buff …

Ionic force field optimization based on single-ion and ion-pair solvation properties: Going beyond standard mixing rules

M Fyta, RR Netz - The Journal of chemical physics, 2012 - pubs.aip.org
Using molecular dynamics (MD) simulations in conjunction with the SPC/E water model, we
optimize ionic force-field parameters for seven different halide and alkali ions, considering a …

A Kirkwood-Buff derived force field for aqueous alkali halides

MB Gee, NR Cox, Y Jiao, N Bentenitis… - Journal of chemical …, 2011 - ACS Publications
A classical nonpolarizable force field is presented for the simulation of aqueous alkali halide
solutions (MX), where M= Li+, Na+, K+, Rb+, and Cs+ and X= F–, Cl–, Br–, and I–, and their …

Kirkwood-Buff integrals from molecular simulation

N Dawass, P Krüger, SK Schnell, JM Simon… - Fluid Phase …, 2019 - Elsevier
Abstract The Kirkwood-Buff (KB) theory provides a rigorous framework to predict
thermodynamic properties of isotropic liquids from the microscopic structure. Several …

Convergence of Kirkwood–Buff integrals of ideal and nonideal aqueous solutions using molecular dynamics simulations

J Milzetti, D Nayar… - The Journal of Physical …, 2018 - ACS Publications
The computation of Kirkwood–Buff integrals (KBIs) using molecular simulations of closed
systems is challenging due to finite system-size effects. One of the problems involves the …

A Kirkwood− Buff derived force field for methanol and aqueous methanol solutions

S Weerasinghe, PE Smith - The Journal of Physical Chemistry B, 2005 - ACS Publications
A force field for the simulation of methanol and aqueous methanol mixtures is presented.
The force field was specifically designed to reproduce the experimental Kirkwood− Buff …