Scalable On-Board Multi-GPU Simulation of Long-Range Molecular Dynamics

Scalable Multi-GPU Simulation of Long-Range Molecular Dynamics

Molecular dynamics simulations allow us to study the behavior of complex biomolecular systems by modeling the pairwise interaction forces between all atoms. Molecular systems are subject to slowly decaying electrostatic potentials, which turn molecular dynamics into an n-body problem. In this paper, we present a parallel and scalable solution to compute long-range molecular forces, based on the...

On-Board Multi-GPU Molecular Dynamics

Molecular dynamics simulations allow us to study the behavior of complex biomolecular systems. These simulations suffer a large computational complexity that leads to simulation times of several weeks in order to recreate just a few microseconds of a molecule’s motion even on high-performance computing platforms. In recent years, state-ofthe-art molecular dynamics algorithms have benefited from...

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

Molecular dynamics simulation and docking studies on the binding properties of several anticancer drugs to human serum albumin

Disposition and transportation of anticancer drugs by human serum albumin (HSA) affects their bioavailability, distribution and elimination. In this study, the interaction of a set of anticancer drugs with HSA was investigated by molecular dynamics and molecular docking simulations. The drugs' activities were analyzed according to their docking scores, binding sites and structural descriptors. ...

Multi-GPU implementation of the lattice Boltzmann method

The lattice Boltzmann method (LBM) is an increasingly popular approach for solving fluid flows in a wide range of applications. The LBM yields regular, data-parallel computations; hence, it is especially well fitted to massively parallel hardware such as graphics processing units (GPU). Up to now, though, single-GPU implementations of the LBM are of moderate practical interest since the on-boar...