Our investigations into efficient molecular dynamics integration
schemes have led to several new directions of research that
may have broader implications to the general biological community. One of them
is our work in developing new mathematical tools for computing and modeling
lattice summations. Lattice sums are relevant to a number of fields
in biology and physics. Two important applications are found in the
evaluation of the electrostatic Coulomb interactions of charged atoms
for molecular dynamics simulation and another is in the reduction of
experimental data from
crystallography studies.
Ewald's method, developed
in 1921, splits an infinite electrostatic summation over a periodic lattice
into direct-space and reciprocal-space terms.
In our work [Batcho & Schlick, 2001b], we have extended this concept
in such a way that the splitting can be optimized to the modeler's
detailed needs. One such example is in the isolation of all near-field
pairwise interactions into the direct term, and all far-field interactions
into the reciprocal term. This type of splitting is expected to have advantages
in applications of multiple timestep schemes for biomolecular
studies.
Go back to "Methods for Macromolecular
Modeling: Overview"