Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

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

NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …

The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐
spline interpolation of the structure factors. This reformulation allows a natural extension of …

NAMD is a parallel molecular dynamics code designed for high‐performance simulation of
large biomolecular systems. NAMD scales to hundreds of processors on high‐end parallel …

Algorithms for the symmetry-adapted energy minimisation of solids using analytical first and
second derivatives have been devised and implemented in a new computer program GULP …

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 …

Standard Ewald sums, which calculate, eg, the electrostatic energy or the force in
periodically closed systems of charged particles, can be efficiently speeded up by the use of …

We investigate pairwise electrostatic interaction methods and show that there are viable
computationally efficient (O (N)) alternatives to the Ewald summation for typical modern …

▪ Abstract Current computer simulations of biomolecules typically make use of classical
molecular dynamics methods, as a very large number (tens to hundreds of thousands) of …