GENESIS: a hybrid‐parallel and multi‐scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations. (7th May 2015)

• Record Type: Journal Article
• Authors: Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji
• Is Part Of: Wiley interdisciplinary reviews. Volume 5:Number 4(2015:Jul./Aug.)
• Page Start: 310
• Page End: 323
• Publication Date: 2015-05-07
• Subjects: Chemistry, Physical and theoretical -- Periodicals; Cheminformatics -- Periodicals; Biochemistry -- Periodicals; 541.220285
• DOI: 10.1002/wcms.1220
• Languages: English
• ISSNs: 1759-0876

Abstract

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 Sci 2015, 5:310–323. doi: 10.1002/wcms.1220 This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Computer and Information Science > Computer Algorithms and Programming Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods Abstract :