Molecular dynamics (MD) has evolved into a ubiquitous, versatile and powerful
computational method for fundamental research in science branches such as biology …

▪ 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 …

ESPResSo is an extensible simulation package for research on soft matter. This versatile
molecular dynamics program was originally developed for coarse-grained simulations of …

The use of accelerators such as graphics processing units (GPUs) has become popular in
scientific computing applications due to their low cost, impressive floating-point capabilities …

The “bottom-up” approach to coarse-graining, for building accurate and efficient
computational models to simulate large-scale and complex phenomena and processes, is …

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 describe a new program package that is designed to perform numerical Molecular
Dynamics (MD) and Monte Carlo (MC) simulations for a broad class of soft matter systems in …

Classical atomistic simulations, also known as molecular mechanics simulations, use simple
potential-energy functions to model molecular systems at the atomic level. In this …

We present the asymptotic transitions from microscopic to macroscopic physics, their
computational challenges and the asymptotic-preserving (AP) strategies to compute …

The bottleneck in classical molecular dynamics (MD) simulations is well known to be the
evaluation of the nonbonded interactions, of which the slowly decaying electrostatic …