Benchmarking MD systems simulations on the graphics processing unit and multi-core systems

摘要

Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core systems are used as solutions to overcome this impediment. The current paper describes a comparison done between these two kinds of systems. The first system used implies the graphics processing unit, respectively CUDA with the OpenMM molecular dynamics package and OpenCL that allows the kernels to run on the GPU. This simulation is done on a new thermostat which mixes the Berendsen thermostat with the Langevin dynamics. The second comprises the molecular dynamics simulation and energy minimization package GROMACS which is based on a parallelization through MPI (Message Passing Interface) on multi-core systems. The second simulation uses another new thermostat algorithm related respectively, dissipative particle dynamics - isotropic type (DPD-ISO). Both thermostats are innovative, based on a new theory developed by us. Results show that parallelization on multi-core systems has a performance up to 33 times greater than the one performed on the graphics processing unit. In both cases temperature of the system was maintained close to the one taken as reference. For the simulation using the CUDA GPU, the faster runtime was obtained when the number of processors was equal to four, the simulation speed being 3.67 times faster compared to the case of only one processor.