GROMACS 3.3.3 scaling for short coarse-grained simulation

I have run short (20ns) coarse-grained MD simulations where system contained:

- 1 Phospholamban pentamer protein (pdb:1ZLL) 255 amino acid residues
- 229 molecules of DPPC phospholipids
- 2454 molecules of water
- 3 Cl- counter ions

with 1, 2, 4 and 8 cores in parallel on my server.


Red line represents linear scaling in perfect world based on performance of one core simulation. Blue line represent polynomial regression line from results for 2, 4 and 8 cores simulations.

My server has two quad-core processors and it looks like that in this case it does not make sense to use more than 4 cores in parallel for one simulation.

If you are interested about result of this short simulation, this is how it looks like in starting point random state in 0 ns and how it looks like after 20 ns simulation.
Water molecules and hydrocarbon lipid chains are not shown for clarity. Color chains represent five amino acid chains of phospholamban protein. Lipid headgroups are represented as colored balls. How you can see lipid bilayer is nicely formed in 20 ns timepoint.

Before I am going to do more scalability tests how to best utilize server hardware I decided to upgrade to Gromacs 4.0 that suppose to have two orders of magnitude better scaling than 3.3 version ...