Highlights of our Work
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Molecular modeling simulates the motion of cellular biomolecules at the
atomic level. To make the simulations faithful, the physical forces
acting between atoms need to be described accurately. Electric field effects
between atoms, so-called atomic polarizabilities, are especially difficult
to model well in a computationally cost effective way. There is an ongoing
effort in the molecular modeling community to develop cost effective models
that more faithfully represent the microscopic properties of biomolecules
due to the ambient electric field effects. Recent development work has added
support in the simulation program
NAMD
for one of these advanced modeling efforts.
As reported,
the new algorithms used in NAMD achieve good parallel computing performance,
with a cost that is not more than twice that of the standard model,
not accounting for atomic polarizabilities. The new model
is demonstrated to reproduce many physical properties better than the
standard model, including more accurate bulk density and surface tension
at the interface between liquids and more accurate diffusive behavior of
ions in a solution. More on our
research webpage.