An efficient molecular dynamics (MD) algorithm is presented in this paper for biomolecular
systems, which incorporates a novel variation on the fast multipole method (FMM) coupled to
the reversible reference system propagator algorithm (r‐RESPA). A top‐down FMM is
proposed which calculates multipoles recursively from the top of the box tree instead of from
the bottom in Greengard's original FMM, in an effort to be more efficient for noncubic or
nonuniform systems. In addition, the use of noncubic box subdivisions of biomolecular …