Molecular dynamics simulation of macromolecules using graphics processing unit

J Xu and Y Ren and W Ge and XA Yu and XZ Yang and JH Li, MOLECULAR SIMULATION, 36, 1131-1140 (2010).

DOI: 10.1080/08927022.2010.506512

Molecular dynamics (MD) simulation is a powerful computational tool to study the behaviour of macromolecular systems. However, many simulations in this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing units (GPUs) have provided unprecedented computational power for scientific applications. Many MD algorithms suit the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU are presented. For validation, we have performed MD simulations of polymer crystallisation with our GPU package, GPU_MD-1.0.5, and the results agree perfectly with computations on CPUs, meanwhile GPU_MD-1.0.5 achieves about 39 times speedup compared with GROMACS-4.0.5 on a single CPU core. Therefore, our single GPU code has already provided an inexpensive alternative for macromolecular simulations of traditional CPU clusters and will serve as a basis for developing parallel GPU programs to further speed up the computations.

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