Efficient Parallelization of Short-Range Molecular Dynamics Simulations on Many-Core Systems

Efficient parallelization of the genetic algorithm solution of traveling salesman problem on multi-core and many-core systems

Efficient parallelization of genetic algorithms (GAs) on state-of-the-art multi-threading or many-threading platforms is a challenge due to the difficulty of schedulation of hardware resources regarding the concurrency of threads. In this paper, for resolving the problem, a novel method is proposed, which parallelizes the GA by designing three concurrent kernels, each of which running some depe...

Efficient parallelization of molecular dynamics simulations with short-ranged forces

Recently, an alternative strategy for the parallelization of molecular dynamics simulations with short-ranged forces has been proposed. In this work, this algorithm is tested on a variety of multi-core systems using three types of benchmark simulations. The results show that the new algorithm gives consistent speedups which are depending on the properties of the simulated system either comparab...

A hybrid algorithm for parallel molecular dynamics simulations

This article describes an algorithm for hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-ranged forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors ...

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

Parallel replica dynamics with a heterogeneous distribution of barriers: application to n-hexadecane pyrolysis.

Parallel replica dynamics simulation methods appropriate for the simulation of chemical reactions in molecular systems with many conformational degrees of freedom have been developed and applied to study the microsecond-scale pyrolysis of n-hexadecane in the temperature range of 2100-2500 K. The algorithm uses a transition detection scheme that is based on molecular topology, rather than energe...