# nwARGOS benchmarks

## SPC/E water

Input files for molecular dynamics simulations of pure water are available for five different system sizes. These systems were chosen to contain 1, 8, 27, 64 and 125 identical boxes of 216 SPC/E water molecules. Since the velocities are also identical in each box, the results of a molecular dynamics simulation should be identical for each of these systems. This not only provides a means of checking proper execution of the code, but also allows for timings as a function of system size.

drop: a molecular dynamics simulation of 216 SPC/E water molecules

bucket: a molecular dynamics simulation of 1,728 SPC/E water molecules

river: a molecular dynamics simulation of 5,832 SPC/E water molecules

sea: a molecular dynamics simulation of 13,824 SPC/E water molecules

ocean: a molecular dynamics simulation of 27,000 SPC/E water molecules

## Myoglobin

As an example of a solvated protein, input files for myoglobin in aqueous solution are available. This system has been used previously in the literature to benchmark parallel molecular dynamics codes.

myo: a molecular dynamics simulation of myoglobin in SPC/E water (10,914 atoms)

## Speedup curves

For selected benchmarks speedup curves are compared as obtained for the KSR-2 and the IBM SP-2.