Development of the trappe force field for ammonia

2010 ◽  
Vol 75 (5) ◽  
pp. 577-591 ◽  
Author(s):  
Ling Zhang ◽  
J. Ilja Siepmann
Keyword(s):  
Dielectric Constant ◽  
Nitrogen Atom ◽  
Force Field ◽  
Electrostatic Interactions ◽  
Hydrogen Atoms ◽  
Site Model ◽  
Lennard Jones ◽  
Hydrogen Position ◽  
Partial Charges ◽  
Vapor Liquid

The transferable potentials for phase equilibria (TraPPE) force field is extended through the development of a non-polarizable five-site ammonia model. In this model, the electrostatic interactions are represented by three positive partial charges placed at the hydrogen position and a compensating partial charge placed on an M site that is located on the C3 molecular axis and displaced from the nitrogen atom toward the hydrogen atoms. The repulsive and dispersive interactions are represented by placing a single Lennard–Jones site at the position of the nitrogen atom. Starting from the five-site model by Impey and Klein (Chem. Phys. Lett. 1984, 104, 579), this work optimizes the Lennard–Jones parameters and the magnitude of the partial charges for three values of the M site displacement. This parameterization is done by fitting to the vapor–liquid coexistence curve of neat ammonia. The accuracy of the three resulting models (differing in the displacement of the M site) is assessed through computation of the binary vapor–liquid equilibria with methane, the structure and the dielectric constant of liquid ammonia. The five-site model with an intermediate displacement of 0.08 Å for the M site yields a much better value for the dielectric constant, whereas differences in the other properties are quite small.

scholarly journals W-RESP: Well-Restrained Electrostatic Potential Derived Charges. Revisiting the Charge Derivation Model

2020 ◽  
Author(s):  
Michal Janeček ◽  
Petra Kührová ◽  
Vojtěch Mlýnský ◽  
Michal Otyepka ◽  
Jiří Šponer ◽  
...  
Keyword(s):  
Force Field ◽  
Electrostatic Potential ◽  
Electrostatic Interactions ◽  
Force Fields ◽  
Amber Force Field ◽  
Heterocyclic Molecules ◽  
Partial Charges ◽  
Grid Points ◽  
Dynamics Simulations ◽  
Extra Point

ABSTRACTRepresentation of electrostatic interactions by a Coulombic pair-wise potential between atom-centered partial charges is a fundamental and crucial part of empirical force fields used in classical molecular dynamics simulations. The broad success of the AMBER force field family originates mainly from the restrained electrostatic potential (RESP) charge model, which derives partial charges to reproduce the electrostatic field around the molecules. However, description of the electrostatic potential around molecules by standard RESP may be biased for some types of molecules. In this study, we modified the RESP charge derivation model to improve its description of the electrostatic potential around molecules, and thus electrostatic interactions in the force field. In particular, we re-optimized the atomic radii for definition of the grid points around the molecule, redesigned the restraining scheme and included extra point charges. The RESP fitting was significantly improved for aromatic heterocyclic molecules. Thus, the suggested W-RESP(-EP) charge derivation model showed clear potential for improving the performance of the nucleic acid force fields, for which poor description of nonbonded interactions, such as underestimated base pairing, makes it difficult to describe the folding free energy landscape of small oligonucleotides.

scholarly journals Molecular simulation of the vapor-liquid equilibria of xylene mixtures: Force field performance, and Wolf vs. Ewald for electrostatic interactions

2019 ◽  
Vol 485 ◽  
pp. 239-247 ◽  
Author(s):  
Sebastián Caro-Ortiz ◽  
Remco Hens ◽  
Erik Zuidema ◽  
Marcello Rigutto ◽  
David Dubbeldam ◽  
...  
Keyword(s):  
Force Field ◽  
Molecular Simulation ◽  
Electrostatic Interactions ◽  
Field Performance ◽  
Vapor Liquid Equilibria ◽  
Vapor Liquid

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>

A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions

2017 ◽  
Vol 146 (5) ◽  
pp. 054501 ◽  
Author(s):  
Julian Michalowsky ◽  
Lars V. Schäfer ◽  
Christian Holm ◽  
Jens Smiatek
Keyword(s):  
Force Field ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Coarse Grained ◽  
Water Model ◽  
Martini Force Field

scholarly journals Molecular Dynamics Simulations of CO2Molecules in ZIF-11 Using Refined AMBER Force Field

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
W. Wongsinlatam ◽  
T. Remsungnen
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Binding Energies ◽  
Hydrogen Atoms ◽  
Amber Force Field ◽  
Bonding Parameters ◽  
Flexible Framework ◽  
Dynamics Simulations

Nonbonding parameters of AMBER force field have been refined based onab initiobinding energies of CO2–[C7H5N2]−complexes. The energy and geometry scaling factors are obtained to be 1.2 and 0.9 forεandσparameters, respectively. Molecular dynamics simulations of CO2molecules in rigid framework ZIF-11, have then been performed using original AMBER parameters (SIM I) and refined parameters (SIM II), respectively. The site-site radial distribution functions and the molecular distribution plots simulations indicate that all hydrogen atoms are favored binding site of CO2molecules. One slight but notable difference is that CO2molecules are mostly located around and closer to hydrogen atom of imidazolate ring in SIM II than those found in SIM I. The Zn-Zn and Zn-N RDFs in free flexible framework simulation (SIM III) show validity of adapting AMBER bonding parameters. Due to the limitations of computing resources and times in this study, the results of flexible framework simulation using refined nonbonding AMBER parameters (SIM IV) are not much different from those obtained in SIM II.

Mining the Cambridge Database for theoretical chemistry. Mi-LJC: a new set of Lennard-Jones–Coulomb atom–atom potentials for the computer simulation of organic condensed matter

CrystEngComm ◽  
2020 ◽  
Vol 22 (43) ◽  
pp. 7350-7360 ◽  
Author(s):  
Angelo Gavezzotti ◽  
Leonardo Lo Presti ◽  
Silvia Rizzato
Keyword(s):  
Computer Simulation ◽  
Force Field ◽  
Condensed Matter ◽  
Molecular Crystals ◽  
Theoretical Chemistry ◽  
Lennard Jones ◽  
Force Field Parametrization

A novel, universal Lennard-Jones–Coulomb (LJC) atom–atom force field parametrization reproduces the experimental sublimation enthalpies of 377 molecular crystals drawn from the CSD.

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