naa a22 4500 510734812 CHVBK 20180411083006.0 cr unu---uuuuu 180411e20130901xx s 000 0 eng 10.1007/s12039-013-0490-y doi (NATIONALLICENCE)springer-10.1007/s12039-013-0490-y GOGA N. Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747, Groningen, AG, The Netherlands aut Simulating chemical systems: MPI and GPU parallelization of novel SD algorithms [Elektronische Daten] [N GOGA] Molecular dynamics is used for simulating chemical systems with the goal of studying a large range of phenomena starting from cell structures to the design of new materials, drugs, etc. A very important component of molecular dynamics is the use of well-suited atomistic and molecular modelling of the chemical systems. This article presents the MPI and GPU-CUDA parallelization of novel stochastic-Langevin dynamics algorithm that is used in molecular dynamics for controlling the temperature of simulated systems. The research has been performed in the Molecular Dynamics Group of the University of Groningen and it is going to be included in the next version of Gromacs tool of molecular dynamics ( www.gromacs.org ). The Langevin algorithm implemented is original and is based on impulse application of friction and noise. Theoretical background, implementation, an efficiency discussion and relevant simulation results are presented in the different sections of this article. The simulations used Martini water. The parallelization of the algorithms was done in two versions: one in MPI using domain decomposition and another version was done in CUDA. Graphical Abstract A very important component of molecular dynamics is the use of well-suited atomistic and molecular modelling of the chemical systems. This article presents the MPI and GPU-CUDA parallelisation of novel stochastic-Langevin dynamics algorithm that is used in molecular dynamics for controlling the temperature of simulated systems. The Langevin algorithm implemented is original and is based on impulse application of friction and noise. Indian Academy of Sciences, 2013 Molecular dynamics nationallicence GPU nationallicence paralelisation nationallicence simulations nationallicence Journal of Chemical Sciences Springer India 125/5(2013-09-01), 1285-1292 0974-3626 125:5<1285 2013 125 12039 https://doi.org/10.1007/s12039-013-0490-y text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s12039-013-0490-y text/html Onlinezugriff via DOI NATIONALLICENCE 100 1- GOGA N. Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747, Groningen, AG, The Netherlands aut NATIONALLICENCE 773 0- Journal of Chemical Sciences Springer India 125/5(2013-09-01), 1285-1292 0974-3626 125:5<1285 2013 125 12039 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer