… of Molecular Dynamics (MD). At present, the main challenge of computational molecular
dynamics … time scale while we are routinely able to do computations on a scale of only one or a …

… methods for molecular dynamics could be taught entirely from this book. For a broader
perspective on molecular simulation … methods that are used for studying molecular dynamics. …

… and ab initio molecular dynamics approaches are discussed. … field and novel molecular
dynamics methods, the mutant T4 … dynamics, the so called ab initio molecular dynamics method, …

Steered molecular dynamics (SMD) induces unbinding of ligands and conformational
changes in biomolecules on time scales accessible to molecular dynamics simulations. Time-…

… molecular dynamics, a class of methods aimed at extending the timescale range of molecular
dynamics, … underpinning the different methods (parallel replica dynamics, hyperdynamics, …

… , when processes need to compute the total force on each atom assigned to them. We adopt
this approach in PuReMD because force computations in ReaxFF are relatively expensive …

… In this paper, we present algorithmic and numerical techniques underlying our implementation
of ReaxFF, called sPuReMD (serial Purdue reactive molecular dynamics program). In …

… Intermediate models are appropriate to answer dynamic problems wherein the accurate
modeling of the backbone dihedrals and formation of backbone hydrogen bonds are required, …

… In this paper, we present a review of ab initio molecular dynamics from a computational
perspective and from first principles. Our main aim is to create a document which is self-contained…

… some of the ways we have been … of molecular simulation, including the concept of
neighborsearching, and we discuss the present and future challenges we see for exascale …