Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

We present a detailed overview of classical molecular simulation studies examining the self-
diffusion coefficient of water. The self-diffusion coefficient is directly associated with the …

Coarse-grained (CG) simulations have become an essential tool to study a large variety of
biomolecular processes, exploring temporal and spatial scales inaccessible to traditional …

A new molecular dynamics model in which the point charges on atomic sites are allowed to
fluctuate in response to the environment is developed and applied to water. The idea for …

A simple treatment for incorporating induced polarization in computer simulations is
formulated on the basis of the classical Drude oscillator model. In this model, electronic …

We report the iAMOEBA (“inexpensive AMOEBA”) classical polarizable water model. The
iAMOEBA model uses a direct approximation to describe electronic polarizability, in which …

We have performed long molecular dynamics simulations of water using four popular water
models, namely simple point charge (SPC), extended simple point charge (SPC/E), and the …

Standard force fields used in biomolecular computing describe electrostatic interactions in
terms of fixed, usually atom-centered, charges. Real physical systems, however, polarize …

The objective of this work is to obtain a water model for simulations of biological
macromolecules in solution. A pragmatic approach is taken in which we use the same type …

Classical atomistic simulations, also known as molecular mechanics simulations, use simple
potential-energy functions to model molecular systems at the atomic level. In this …