Fast parallel algorithms for short-range molecular dynamics
Journal of Computational Physics
NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Molecular Modeling and Simulation: An Interdisciplinary Guide
Molecular Modeling and Simulation: An Interdisciplinary Guide
GPU accelerated molecular dynamics simulation of thermal conductivities
Journal of Computational Physics
Mollified Impulse Methods for Highly Oscillatory Differential Equations
SIAM Journal on Numerical Analysis
GPU acceleration of cutoff pair potentials for molecular modeling applications
Proceedings of the 5th conference on Computing frontiers
Smoothed Particle Hydrodynamics Simulations on Multi-GPU Systems
PDP '12 Proceedings of the 2012 20th Euromicro International Conference on Parallel, Distributed and Network-based Processing
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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-of-the-art molecular dynamics algorithms have benefited from the parallel computing capabilities of multicore systems, as well as GPUs used as co-processors. In this paper we present a parallel molecular dynamics algorithm for on-board multi-GPU architectures. We parallelize a state-of-the-art molecular dynamics algorithm at two levels. We employ a spatial partitioning approach to simulate the dynamics of one portion of a molecular system on each GPU, and we take advantage of direct communication between GPUs to transfer data among portions. We also parallelize the simulation algorithm to exploit the multi-processor computing model of GPUs. Most importantly, we present novel parallel algorithms to update the spatial partitioning and set up transfer data packages on each GPU. We demonstrate the feasibility and scalability of our proposal through a comparative study with NAMD, a well known parallel molecular dynamics implementation.