Systematic Benchmarking of Large Molecular Dynamics Simulations Employing GROMACS on Massive Multiprocessing Facilities

The influence of the total number of cores, the number of cores dedicated to Particle mesh Ewald (PME) calculation and the choice of single vs. double precision on the performance of molecular dynamic (MD) simulations in the size of 70,000 to 1.7 million of atoms was analyzed on three different high-performance computing facilities employing GROMACS 4 by running about 6000 benchmark simulations. Small and medium sized systems scaled linear up to 64 and 128 cores, respectively. Systems with half a million to 1.2 million atoms scaled linear up to 256 cores. The best performance was achieved by dedicating 25% of the total number of cores to PME calculation. Double precision calculations lowered the performance by 30-50%. A database for collecting information about MD simulations and the achieved performance was created and is freely available online and allows the fast estimation of the performance that can be expected in similar environments. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 32: 600-606, 2011