title: GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.
abstract: GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models.WIREs Comput Mol Sci2015, 5:310-323. doi: 10.1002/wcms.1220.
authors.affiliation: Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science Kobe, Japan.
authors.forename: Jaewoon
authors.initials: J
authors.lastname: Jung
authors.affiliation: Theoretical Molecular Science Laboratory, RIKEN Wako-shi, Japan.
authors.forename: Takaharu
authors.initials: T
authors.lastname: Mori
authors.affiliation: Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science Kobe, Japan.
authors.forename: Chigusa
authors.initials: C
authors.lastname: Kobayashi
authors.affiliation: Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science Kobe, Japan.
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Matsunaga
authors.affiliation: Nagahama Institute of Bio-Science and Technology Nagahama, Japan.
authors.forename: Takao
authors.initials: T
authors.lastname: Yoda
authors.affiliation: Department of Biochemistry and Molecular Biology, and Department of Chemistry, Michigan State University East Lansing, MI, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Feig
authors.affiliation: Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science Kobe, Japan; Theoretical Molecular Science Laboratory, RIKEN Wako-shi, Japan; Interdisciplinary Theoretical Science Research Group, RIKEN Wako-shi, Japan; Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center Kobe, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Sugita