Performance Analysis of Different Computational Architectures: Molecular Dynamics in Application to Protein Assemblies, Illustrated by Microtubule and Electron Transfer Proteins

All-atom molecular dynamics simulation represents a computationally challenging, but powerful approach for studying conformational changes and interactions of biomolecules and their assemblies of different kinds. Usually, the numbers of simulated particles in modern molecular dynamics studies range from thousands to tens of millions, while the simulated timescales span from nanoseconds to microseconds. For cost and computation efficiency, it is important to determine the optimal computer hardware for simulations of biomolecular systems of different sizes and timescales. Here we compare performance and scalability of 17 commercially available computational architectures, using molecular dynamics simulations of water and two different protein systems in GROMACS-5 package as computing benchmarks. We report typical single-node performance of various combinations of modern CPUs and GPUs, as well as multiple-node performance of “Lomonosov-2” supercomputer in molecular dynamics simulations of different protein systems in nanoseconds per day. These data can be used as practical guidelines for selection of optimal computer hardware for various molecular dynamics simulation tasks.