Journal
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
Volume 5, Issue 4, Pages 310-323Publisher
WILEY
DOI: 10.1002/wcms.1220
Keywords
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Funding
- RIKEN Advanced Institute for Computational Science through the HPCI System Research project [ra000009, hp120060, hp120309, hp130003, hp140091, hp140169, hp140229]
- High Performance Computing Infrastructure (HPCI) Strategic Program of the Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- [26119006]
- Direct For Biological Sciences
- Div Of Molecular and Cellular Bioscience [1330560] Funding Source: National Science Foundation
- Grants-in-Aid for Scientific Research [26119006, 26120533] Funding Source: KAKEN
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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 NPT 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. (C) 2015 The Authors. WIREs Computational Molecular Science published by John Wiley & Sons, Ltd.
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