scholarly journals Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field

2010 ◽  
Vol 6 (4) ◽  
pp. 1181-1198 ◽  
Author(s):  
Christopher M. Baker ◽  
Pedro E. M. Lopes ◽  
Xiao Zhu ◽  
Benoît Roux ◽  
Alexander D. MacKerell
Keyword(s):  
Force Field ◽  
Free Energies ◽  
Accurate Calculation ◽  
Polarizable Force Field ◽  
Lennard Jones

scholarly journals Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field

2016 ◽  
Vol 37 (32) ◽  
pp. 2749-2758 ◽  
Author(s):  
Noor Asidah Mohamed ◽  
Richard T. Bradshaw ◽  
Jonathan W. Essex
Keyword(s):  
Force Field ◽  
Small Molecules ◽  
Free Energies ◽  
Polarizable Force Field ◽  
Solvation Free Energies

scholarly journals Calculating binding free energies of host–guest systems using the AMOEBA polarizable force field

2016 ◽  
Vol 18 (44) ◽  
pp. 30261-30269 ◽  
Author(s):  
David R. Bell ◽  
Rui Qi ◽  
Zhifeng Jing ◽  
Jin Yu Xiang ◽  
Christopher Mejias ◽  
...  
Keyword(s):  
Force Field ◽  
Free Energies ◽  
Polarizable Force Field ◽  
Guest Binding ◽  
Binding Free Energies

Cucurbit[7]uril host–guest binding free energies are investigated using the AMOEBA polarizable force field.

Hydration Free Energies of Organic Molecules in the FreeSolv Database Calculated with Polarized Atom In Molecules Atomic Charges and the GAFF Force Field.

2018 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Alejandro Lara ◽  
David L. Mobley ◽  
Toon Vestraelen ◽  
Adelio R Matamala ◽  
...  
Keyword(s):  
Force Field ◽  
Functional Groups ◽  
Electrostatic Interactions ◽  
Organic Molecules ◽  
Force Fields ◽  
Chemical Elements ◽  
Atomic Charges ◽  
Free Energies ◽  
Molecular Systems ◽  
Solvent Model

<div>Computer simulations of bio-molecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in bio-molecular systems and are therein described by atomic point charges.</div><div>In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the MBIS atomic charge method, including the solvent polarization, with a root mean square error of 2.0 kcal mol<sup>-1</sup> for the 613 organic molecules studied. The largest deviation was observed for phosphor-containing molecules and the molecules with amide, ester and amine functional groups.</div>

Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model

1999 ◽  
Vol 110 (2) ◽  
pp. 741-754 ◽  
Author(s):  
Jay L. Banks ◽  
George A. Kaminski ◽  
Ruhong Zhou ◽  
Daniel T. Mainz ◽  
B. J. Berne ◽  
...  
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Point Charge ◽  
Point Charge Model ◽  
Polarizable Force Field ◽  
Charge Model

Free Energies of Hydration from a Generalized Born Model and an All-Atom Force Field

2004 ◽  
Vol 108 (41) ◽  
pp. 16264-16270 ◽  
Author(s):  
William L. Jorgensen ◽  
Jakob P. Ulmschneider ◽  
Julian Tirado-Rives
Keyword(s):  
Force Field ◽  
Free Energies ◽  
Generalized Born ◽  
Born Model ◽  
Generalized Born Model
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