Code modernization strategies for short-range non-bonded molecular dynamics simulations

Molecular dynamics computer simulations of solvation in hydrogen bonded systems

This review first discusses briefly some of he various models used in large scale computer simulations of water and aqueous systems. The radial pair distribution functions describing the structures of the hydration shells of divalent ions, as determined from MD simulations of 1.lm solutions of the chloride salts, are then presented. The ion-water potentials for these studies were determined by ...

Explicit design of FPGA-based coprocessors for short-range force computations in molecular dynamics simulations

FPGA-based acceleration of molecular dynamics simulations (MD) has been the subject of several recent studies. The short-range force computation, which dominates the execution time, is the primary focus. Here we combine: a high level of FPGA-specific design including cell lists, systematically determined interpolation and precision, handling of exclusion, and support for MD simulations of up to...

Communication: Truncated non-bonded potentials can yield unphysical behavior in molecular dynamics simulations of interfaces.

Non-bonded potentials are included in most force fields and therefore widely used in classical molecular dynamics simulations of materials and interfacial phenomena. It is commonplace to truncate these potentials for computational efficiency based on the assumption that errors are negligible for reasonable cutoffs or compensated for by adjusting other interaction parameters. Arising from a meta...

Long Range Corrections to the Vapor-Liquid Equilibrium and Surface Tension of Methane with NVT Molecular Dynamics Simulations

Fast Parallel Algorithms for Short–Range Molecular Dynamics

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–atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently — those with short–range forces wher...