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The generation of bond, angle, and torsion parameters for classical molecular dynamics force fields typically requires fitting parameters such that classical properties such as energies and gradients match precalculated quantum data for structures that scan the value of interest. We present a program, Paramfit, distributed as part of the AmberTools software package that automates and extends this fitting process, allowing for simplified parameter generation for applications ranging from single molecules to entire force fields. Paramfit implements a novel combination of a genetic and simplex algorithm to find the optimal set of parameters that replicate either quantum energy or force data. The program allows for the derivation of multiple parameters simultaneously using significantly fewer quantum calculations than previous methods, and can also fit parameters across multiple molecules with applications to force field development. Paramfit has been applied successfully to systems with a sparse number of structures, and has already proven crucial in the development of the Assisted Model Building with Energy Refinement Lipid14 force field. © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Simulations using ab initio quantum mechanical charge field molecular dynamics (QMCF MD) and classical molecular dynamics using two-body and three-body potentials were performed to investigate the hydration of the Ca2+ ion at different temperatures. Results from the simulations demonstrate significant effects of temperature on solution dynamics and the corresponding composition and structure of hydrated Ca2+. Substantial increase in ligand exchange events was observed in going from 273.15 K to 368.15 K, resulting in a redistribution of coordination numbers to lower values. The effect of temperature is also visible in a red-shift of the ion-oxygen stretching frequencies, reflecting weakened ligand binding. Even the moderate increase from ambient to body temperature leads to significant changes in the properties of Ca2+ in aqueous environment. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [ABSTRACT FROM AUTHOR]