A historical perspective on the application of molecular dynamics (MD) to biological
macromolecules is presented. Recent developments combining state-of-the-art force fields …

Generalized Born (GB) models provide an attractive way to include some thermodynamic
aspects of aqueous solvation into simulations that do not explicitly model the solvent …

OpenMM is a software toolkit for performing molecular simulations on a range of high
performance computing architectures. It is based on a layered architecture: the lower layers …

Δ 9-Tetrahydrocannabinol (THC) and cannabidiol (CBD) occur naturally in marijuana
(Cannabis) and may be formulated, individually or in combination in pharmaceuticals such …

We describe here a general Amber force field (GAFF) for organic molecules. GAFF is
designed to be compatible with existing Amber force fields for proteins and nucleic acids …

In molecular mechanics (MM) studies, atom types and/or bond types of molecules are
needed to determine prior to energy calculations. We present here an automatic algorithm of …

In this study, we present conformational energies for a molecular mechanical model
(Parm99) developed for organic and biological molecules using the restrained electrostatic …

A new derivation of the GLYCAM06 force field, which removes its previous specificity for
carbohydrates, and its dependency on the AMBER force field and parameters, is presented …

Molecular docking is a key tool in structural molecular biology and computer-assisted drug
design. The goal of ligand—protein docking is to predict the predominant binding mode (s) …

The AM1‐BCC method quickly and efficiently generates high‐quality atomic charges for use
in condensed‐phase simulations. The underlying features of the electron distribution …