Consider the best order in which to answer these questions, utilizing an instance of the GROMACS package built with MPICH .

1) Which calculation performed by mdrun takes the majority of the wall time?

2) Find the mean and standard deviation of the "Total Energy" parameter for the villin molecular system over 6 runs of 100000 steps at 0.001 time resolution.

3) How many atoms are in the system?

4) Determine the fastest setup to run that configuration on BobSCEd with a maximum of 16 cores (i.e., 4 nodes x 4 cores/node) over gigabit ethernet. Calculate the speedup compared to a 1 core run for that configuration.

5) For the fastest setup from 4) how much of a difference in wall-time does running the simulation over Infiniband make as compared to gigabit Ethernet? Calculate the speedup compared to a 1 core run (also over Infiniband) for that configuration.

Resources:
*GROMACS site