Combining a polarizable force-field and a coarse-grained polarizable solvent model. II. Accounting for hydrophobic effects

2011 ◽  
Vol 32 (12) ◽  
pp. 2664-2678 ◽  
Author(s):  
Michel Masella ◽  
Daniel Borgis ◽  
Philippe Cuniasse
Keyword(s):  
Force Field ◽  
Coarse Grained ◽  
Polarizable Force Field ◽  
Hydrophobic Effects ◽  
Solvent Model

A coarse-grained polarizable force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate

2017 ◽  
Vol 29 (50) ◽  
pp. 504004 ◽  
Author(s):  
Johannes Zeman ◽  
Frank Uhlig ◽  
Jens Smiatek ◽  
Christian Holm
Keyword(s):  
Ionic Liquid ◽  
Force Field ◽  
Coarse Grained ◽  
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>

Martini 3: a coarse-grained force field with an eye for atomic detail

2021 ◽  
Author(s):  
H. Jelger Risselada
Keyword(s):  
Force Field ◽  
Coarse Grained

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

scholarly journals Martini Coarse-Grained Force Field: Extension to RNA

2017 ◽  
Vol 113 (2) ◽  
pp. 246-256 ◽  
Author(s):  
Jaakko J. Uusitalo ◽  
Helgi I. Ingólfsson ◽  
Siewert J. Marrink ◽  
Ignacio Faustino
Keyword(s):  
Force Field ◽  
Field Extension ◽  
Coarse Grained

Molecular Dynamics Study of Hydration in Ethanol−Water Mixtures Using a Polarizable Force Field†

2005 ◽  
Vol 109 (14) ◽  
pp. 6705-6713 ◽  
Author(s):  
Sergei Yu. Noskov ◽  
Guillaume Lamoureux ◽  
Benoît Roux
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Polarizable Force Field

scholarly journals 2P044 Comparative simulations of protein-ligand binding processes using the MARTINI coarse-grained force field(01B. Protein: Structure & Function,Poster)

2013 ◽  
Vol 53 (supplement1-2) ◽  
pp. S166
Author(s):  
Tatsuki Negami ◽  
Tohru Terada ◽  
Kentaro Shimizu
Keyword(s):  
Protein Structure ◽  
Ligand Binding ◽  
Force Field ◽  
Structure Function ◽  
Coarse Grained
Sign in / Sign up

Export Citation Format

Share Document