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GENESIS: a hybrid‐parallel and multi‐scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

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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 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
The hybrid (MPI + OpenMP) parallelization scheme in SPDYN. (a) Design of the hybrid parallelization of real space interaction in SPDYN. Adjacent cells for send/receive communication are colored by gray, and MPI communications are shown as black arrows. Midpoint candidate cells for cell pairs (a,b) and (c,d) are colored by green. (b) Two‐dimensional views of charge‐grid assignment in SPDYN and other MD programs using slab or pencil decomposition FFT.
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REMD simulations of POPC/DMPC mixed lipid bilayers. (a) Snapshots in the MD simulation at T = 303.15 K and P = 1 atm (upper panels), and snapshots in the T‐REMD simulation at T = 303.15 K and P = 1 atm (lower panels). POPC and DMPC are coloured by blue and cyan, respectively. Structures in unit and image cells are shown together. (b) Mean‐square displacements (MSD) of POPC lipids (left panel) and DMPC lipids (right panel) in MD, T‐REMD, γ‐REMD, and γT‐REMD. MSD is computed for each replica and averaged over all replicas. (c) Histogram of degree of mixing (number of POPC–DMPC contact pairs) at T = 303.15 K and γ = 0 dyn/cm in MD, T‐REMD, γ‐REMD, and γT‐REMD.
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Benchmark performance of MD simulations of (a) DHFR, (b) ApoA1, and (c) STMV on PC clusters, and (d) STMV, macromolecular crowding systems consisting of (e) 11.7 million atoms and (f) 103.7 million atoms on K computer.
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File input/output in GENESIS. (a) Scheme in standard MD simulations. PDB, Protein Data Bank; PSF, Protein Structure File; PAR, Parameter; RST, restart file. Coordinates and velocities are generated in the standard DCD file format. (b) Scheme in REMD simulations. REM, parameter index file. (c) Scheme in large‐scale MD simulations. PRST, parallel restart files; PCRD, parallel coordinates files.
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