The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class bio-molecular dynamics (MD) simulation program designed specifically for GPUs which is able to achieve supercomputing scale performance of 40 nanoseconds/day for all-atom protein systems with over 23, 000 atoms. We illustrate the characteristics of the code, its validation and performance. We also run a microsecond-long trajectory for an all-atom molecular system in explicit TIP3P water on a single workstation computer equipped with just 3 GPUs. This performance on cost effective hardware allows ACEMD to reach microsecond timescales routinely with important implications in terms of scientific applications.

Using a molecular dynamics and mean field theory approach which explicitly accounts for free ions, we study the conformation of polyelectrolyte dendrimers for different generation numbers, spacer lengths, charge distributions and ionic strengths. We find that, due to local charge neutrality, electrostatic interactions are strongly screened under all the conditions studied (including salt free conditions). This leads to the cores of the dendrimers being filled and to a very weak dependence of dendrimer conformations on ionic strength. These results are contrary the predictions of Debye-Hu ¨ckel theory and highlight the limitations of Debye-Hu ¨ckel theory in modeling the properties of highly charged macromolecular systems. However, our simulations suggest that some responsiveness to ionic strength may be recovered for more weakly charged dendrimers.