scholarly journals Implementação dos parâmetros da quitosana no campo de força OPLS-AA para simulações da quitosana por dinâmica molecular

2020 ◽  
Author(s):  
Lourival Rodrigues de Sousa Neto ◽  
Roberto Ribeiro Faria ◽  
Victor de Sousa Batista ◽  
Keli Cristina Barbosa dos Reis ◽  
Eduardo de Faria Franca
Keyword(s):  
Molecular Structure ◽  
Molecular Dynamics ◽  
Dft Calculations ◽  
Structural Optimization ◽  
Force Field ◽  
Structural Stability ◽  
Atomic Charges ◽  
Base Function ◽  
B3lyp Functional ◽  
Partial Atomic Charges

In this work, the molecular dynamics of the finite biopolymer of chitosan in the force field OPLS-AA was made. DFT calculations for structural optimization were performed in the ORCA program with the B3LYP functional and 6-31G base function. The partial atomic charges of Chitosan were obtained by the RESP methodology. The molecular structure of chitosan was structurally evaluated in terms of RMSD and ring overlap. A comparison between the chitosan parameters in OPLS-AA and GROMOS53a6 force-field indicated that in OPLS-AA energy and structural stability are achieved more quickly. The results obtained are in accordance with reports in the literature for this molecule in the GROMOS53A6 force field.

scholarly journals Inclusion of the Most Important Multi-Particle Interactions in the Amber Force Field and Application of the Revised Force Field To Molecular Dynamics Calculations

2015 ◽  
Vol 10 (2) ◽  
pp. 427-435 ◽  
Author(s):  
Н.К. Балабаев ◽  
N.K. Balabaev
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Dynamics Simulation ◽  
Particle Interactions ◽  
Covalent Bonds ◽  
New Members ◽  
Nonbonded Interactions ◽  
Amber Force Field ◽  
Molecular Dynamics Calculations ◽  
Partial Atomic Charges

Formulas for calculation of energy and forces in the new force field of nonbonded interactions including along with traditional members, the polarization, induced by partial atomic charges, and three-particle dispersive interactions of the atoms with covalent bonds are received. The corresponding new members are added to a standard AMBER force field. Molecular dynamics calculations with the use of the updated force field are carried out. It is shown that additional physically reasonable members, taking into account the major three-particle interactions, not strongly slow down molecular dynamics simulation.

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>

scholarly journals Modulating the thermal and structural stability of gallenene via variation of atomistic thickness

2021 ◽  
Author(s):  
Stephanie Lambie ◽  
Krista G. Steenbergen ◽  
Nicola Gaston
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Structural Stability ◽  
Variable Thickness

Using ab initio molecular dynamics, we show that a recently discovered form of 2D Ga—gallenene—exhibits highly variable thickness dependent properties.

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