Classical molecular dynamics has been successfully used to
model structural and dynamic properties of complex biological
systems. However, these methods cannot simulate chemical reactions,
which are essential components of biochemical processes. This is one
of the major drawbacks, limiting the scope and application of molecular
dynamics techniques. Recently, van Duin et al. have proposed a novel
force field, ReaXFF, that aims to mimic chemical reactions using
molecular dynamics. This is achieved by establishing relation between
bond distance, bond order, and bond energy to accurately model
association and dissociation of chemical bonds. Other valence
terms in the force field (angle and torsion) are defined in terms of
the same bond orders to produce correct behavior with association or
dissociation of chemical bonds. ReaXFF also incorporates Coulomb
and Morse potentials to describe non--bonded interactions between all
atoms. The most compute-intensive part of ReaX-based molecular
dynamics is the determination of partial charges on atoms involved
in chemical reactions. This in turn requires the solution of a dense
linear system of equations. Using our prior work on multipole
methods, we develop extremely efficient preconditioned iterative
solvers for computing partial charges. Since these solvers are
invoked at each time-step, the resulting improvement in speed is critical
to the use of ReaX force fields in real applications. We demonstrate
the computational efficiency and modeling accuracy of our methods
in the context of real bio-physical systems.




[* Will you please add few lines about GMRES and Multipole
expansion and how it is used in this context? *]

