A Parallelization Scheme for New DPD-B Thermostats

This paper presents the MPI parallelization of a new algorithm—DPD-B thermostat—for molecular dynamics simulations. The presented results are using Martini Coarse Grained Water System. It should be taken into account that molecular dynamics simulations are time consuming. In some cases the running time varies from days to weeks and even months. Therefore, parallelization is one solution for reducing the execution time. The paper describes the new algorithm, the main characteristics of the MPI parallelization of the new algorithm, and the simulation performances. 1. Introduction Molecular simulation (MD) is a useful tool for studying the physicchemical properties of molecular systems. Nowadays, MD is one method used by the scientific community to analyze the properties of polymers, proteins, lipids, and other cellular systems. It is also used as an alternative to the laboratory experiments for the design of new materials. Molecular dynamics is based on the Newtonian equations of motions. The purpose of this paper is to present an MPI parallelization of a new molecular dynamics algorithm DPD-B that resulted from the combination of a dissipative particle dynamics (DPD) algorithm [1] with Berendsen (B) thermostat [2]. It should be taken into account that molecular dynamics simulations are time consuming. In some cases the running time varies from days to weeks and even months. Therefore, parallelization is one solution for reducing the execution time. This paper describes the new algorithm, the main characteristics of the MPI parallelization of the new algorithm, and the simulation performances. The work was done through research collaboration between Molecular Dynamics Group, University of Groningen, one of the well-known groups in the MD domain, and researchers from Politehnica University of Bucharest. The parallelization was done in Gromacs [3, 4], an open-source software from this domain used worldwide in universities and companies. It should be noted that, ideally, force fields used in molecular dynamics to describe particle interactions should be calibrated such that the desired reference temperature of a simulated system be maintained. However, in practice the average temperature of a simulated system deviates from the desired reference temperature. Therefore thermostats are used for assuring that a simulated system will maintain the reference temperature. Global thermostats apply a collective correction to all particles of a system while dissipative particle dynamics applies temperature corrections to pairs of particles. In this paper we present the