AFMM: A Molecular Mechanics Force Field Parametrization Program
نویسنده
چکیده
منابع مشابه
Robustness in the fitting of molecular mechanics parameters
Automated methods for force field parametrization have attracted renewed interest of the community, but the robustness issues associated with the often ill-conditioned nature of parameter optimization have been vastly underappreciated in the recent literature. For this reason, this article offers a detailed description of the origin and nature of these issues. This includes a discussion of the ...
متن کاملInvestigation of Different Solvents and Temperatures Effects on (3,7) Single-Walled Carbon Nanotubes: DFT Study
In this research, we have studied the structural propenies of water. methanol and ethanol surrounding snidewalledcarbon nanotube (SWCNT) and mixed of them either and we have investigated the solvent effects onthe relative energies and dipole moment values by ming molecular dynamics simulation. We used differentforce field it, deterrnaned energy and other type of geometrical parameters, on the p...
متن کاملOn the transferability of hydration-parametrized continuum electrostatics models to solvated binding calculations
Using molecular mechanics force field partial atomic charges, we show the nonuniqueness of the parametrization of continuum electrostatics models with respect to solute atomic radii and interior dielectric constant based on hydration (vacuum-to-water transfer) free energy data available for small molecules. Moreover, parameter sets that are optimal and equivalent for hydration free energy calcu...
متن کاملProtein structure prediction force fields: parametrization with quasi-newtonian dynamics.
We present an unusual method for parametrizing low-resolution force fields of the type used for protein structure prediction. Force field parameters were determined by assigning each a fictitious mass and using a quasi-molecular dynamics algorithm in parameter space. The quasi-energy term favored folded native structures and specifically penalized folded nonnative structures. The force field wa...
متن کاملParametrization and validation of a force field for liquid-crystal forming molecules.
First principles density functional calculations have been carried out to determine the structures and conformational energies of a series of liquid-crystal fragment molecules. The calculations have been used to derive a molecular mechanics force field that describes a subset of commonly occurring liquid-crystal molecules. The force field has been used to carry out molecular dynamics simulation...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره شماره
صفحات -
تاریخ انتشار 2017