Molecular dynamics (MD) simulation is a powerful computational tool to study
the behavior of macromolecular systems. But many simulations of this field are
limited in spatial or temporal scale by the available computational resource.
In recent years, graphics processing unit (GPU) provides unprecedented
computational power for scientific applications. Many MD algorithms suit with
the multithread nature of GPU. In this paper, MD algorithms for macromolecular
systems that run entirely on GPU are presented. Compared to the MD simulation
with free software GROMACS on a single CPU core, our codes achieve about 10
times speed-up on a single GPU. For validation, we have performed MD
simulations of polymer crystallization on GPU, and the results observed
perfectly agree with computations on CPU. Therefore, our single GPU codes have
already provided an inexpensive alternative for macromolecular simulations on
traditional CPU clusters and they can also be used as a basis to develop
parallel GPU programs to further speedup the computations.Comment: 21 pages, 16 figure
