The simulation of large macromolecular systems has been and remains a challenging
problem. There is a general presumption that simulations carried in periodic boundary …

Empirical force field‐based studies of biological macromolecules are becoming a common
tool for investigating their structure–activity relationships at an atomic level of detail. Such …

Three parallel algorithms for classical molecular dynamics are presented. The first assigns
each processor a fixed subset of atoms; the second assigns each a fixed subset of inter …

An N· log (N) method for evaluating electrostatic energies and forces of large periodic
systems is presented. The method is based on interpolation of the reciprocal space Ewald …

A general all-atom force field for atomistic simulation of common organic molecules,
inorganic small molecules, and polymers was developed using state-of-the-art ab initio and …

Ab initio quantum chemistry has emerged as an important tool in chemical research and is
appliced to a wide variety of problems in chemistry and molecular physics. Recent …

New atom‐and group‐based spherical‐cutoff methods have been developed for the
treatment of nonbonded interactions in molecular dynamics (MD) simulation. A new atom …

Although many types of ancient bacteria and archea rely on hydrogen sulfide (H2S) for their
energy production, eukaryotes generate ATP in an oxygen-dependent fashion. We …

In this article, a recently proposed method called the particle mesh Ewald (PME) method for
computing the long ranged Coulomb interactions in for example molecular dynamics …

A new version of the Fast Multipole Method for the Laplace equation in three dimensions Page
1 ActaNumerica (1997), pp. 229-269 © Cambridge University Press, 1997 A new version of the …