Studying Solvation of Small Biomolecules via Molecular Dynamics using a Polarizable Force Field
نویسندگان
چکیده
منابع مشابه
Ion solvation thermodynamics from simulation with a polarizable force field.
Thermodynamic measurements of the solvation of salts and electrolytes are relatively straightforward, but it is not possible to separate total solvation free energies into distinct cation and anion contributions without reference to an additional extrathermodynamic assumption. The present work attempts to resolve this difficulty using molecular dynamics simulations with the AMOEBA polarizable f...
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Body's iterative force-field computer program has been used to calculate strain energies in cyclooctanone (I). 348 MHZ 1H NMR spectra of (I) have been investigated over the temperature range of 25° to -160°C. Two conformation processes affect the 1H NMR spectrum of (I). Iterative force-field calculations on the conformations and conformational interconversion paths of ...
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The effects of electronic polarization in biomolecular interactions will differ depending on the local dielectric constant of the environment, such as in solvent, DNA, proteins, and membranes. Here the performance of the AMOEBA polarizable force field is evaluated under nonaqueous conditions by calculating the solvation free energies of small molecules in four common organic solvents. Results a...
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In this work, the thermal reaction of aluminum (Al) and nickel oxide (NiO) was investigated by molecular dynamics simulations. Some effective features of reaction such as reaction temperature, the reaction mechanism, and diffusion rate of oxygen into aluminum structure were studied. ReaxFF force field was performed to study the Al/NiO thermite reaction behavior at five different temperatures (5...
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In all of the classical force fields, electrostatic interaction is simply treated and explicit electronic polarizability is neglected. The condensed-phase polarization, relative to the gas-phase charge distributions, is commonly accounted for in an average way by increasing the atomic charges, which remain fixed throughout simulations. Based on the lipid polarizable force field DMPC and followi...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2017
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2016.11.2688