A Highly Extensible Framework for Molecule Dynamic Simulation on GPUs

Xiao Zhang, Wan Guo, Xiao Qin, Xiaonan Zhao
School of Computer Science Northwestern Polytechnical University 127 Youyi xi Road, Xi’an Shaanxi China
The 2013 International Conference on Parallel and Distributed, Processing Techniques and Applications (PDPTA’13), 2013


   title={A Highly Extensible Framework for Molecule Dynamic Simulation on GPUs},

   author={Zhang, Xiao and Guo, Wan and Qin, Xiao and Zhao, Xiaonan},



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Molecular dynamics (MD) was widely used in chemistry and bio molecules. Numerous attempts have been made to accelerate MD simulations. CUDA enabled NVIDIA Graphics processing units (GPUs) use as a general purpose parallel computer chips as CPU. But it is not easy to port a program to GPU. We present a highly extensible framework for molecular dynamics simulation. And we discuss how to accelerate the process of port to GPU. We introduce how to find the performance battle and how to port the time costly procedure to GPU. We discuss about how to decrease the memory usage in GPU and how to improve the maintenance of molecular dynamics simulation. At last, we present the performance of linear and parallel simulation with different number of molecules. Source codes can be found at https://github.com/orlandoacevedo/MCGPU.
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