GPU-based Molecular Dynamics Potential Function And Structural Characteristic Simulation System

GPU (Graphics Processing Unit) has a strong parallel computing capabilities, espe-cially CUDA (Compute Unified Device Architecture) makes the GPU appear to occupyanincreasinglyimportantpositioninHigh-PerformanceComputing. MolecularDynamicssimulation technique is the use of a computer system to simulate the motion of individualparticles. As the simulation time is very long due to its large amount of calculation, it’sconsidered to compute Molecular Dynamics Simulation into GPU.BasedontheanalysisofparallelismofGPUandtheprincipleofMolecularDynamicssimulation,themosttime-consumingprocesssimulationfunctiontocalculatethepotentialmove to GPU computing. With analyzing potential function to calculate the intrinsic par-allelism using CUDA threads and particles the one relationship, combined with the GPUwith its own characteristics, to accelerate the completion of the calculation. This paperimplementstwopairpotentials(Morsepotential, Lennard-Jonespotential), andtwomulti-body potentials (Tersoff potential, EAM potential) on GPU accelerated computing. Theresults show that using NVIDIA GeForce GTX650’s GPU, relative to Intel Core2E7500CPU, the acceleration ratio of potential function to calculate is between22to91, whichalso will be able to greatly shorten the time of calculation of entire molecular dynamicssimulations. This paper also describes acceleration of two structural characteristics(radialdistribution function(RDF), and static structure factor(SSF)), the results show that underthe same platform with the above, the acceleration ratio is between22to27.Finally, under the Windows platform, using Qt graphical user interface design, thispaper builds a molecular dynamics simulation system, in which the amount of the poten-tial function and structural characteristics of GPU-based computing to run, and the systemwas verified.