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

Jung J, Mori T, Kobayashi C, Matsunaga Y, Yoda T, Feig M, Sugita Y - Wiley Interdiscip Rev Comput Mol Sci (2015)

Bottom Line: 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.WIREs Comput Mol Sci 2015, 5:310-323. doi: 10.1002/wcms.1220.

View Article: PubMed Central - PubMed

Affiliation: Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science Kobe, Japan.

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.

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Related in: MedlinePlus

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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fig02: 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.

Mentions: To perform simulations with GENESIS, users first prepare PDB (Protein Data Bank), PSF (Protein Structure File), and PAR (PARameter) files as input. The PSF file can be generated with PSFGEN supplied with NAMD,13 VMD,85 CHARMM,11 or with other tools. The PAR file is expected to be in standard CHARMM format. During simulations, trajectory files (coordinates and velocities) in standard DCD format are generated as output (Figure 2(a)). A restart file (RST) that contains atomic coordinates, velocities, box size, thermostat momenta, and barostat momenta is also written out.


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

Jung J, Mori T, Kobayashi C, Matsunaga Y, Yoda T, Feig M, Sugita Y - Wiley Interdiscip Rev Comput Mol Sci (2015)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4696414&req=5

fig02: 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.
Mentions: To perform simulations with GENESIS, users first prepare PDB (Protein Data Bank), PSF (Protein Structure File), and PAR (PARameter) files as input. The PSF file can be generated with PSFGEN supplied with NAMD,13 VMD,85 CHARMM,11 or with other tools. The PAR file is expected to be in standard CHARMM format. During simulations, trajectory files (coordinates and velocities) in standard DCD format are generated as output (Figure 2(a)). A restart file (RST) that contains atomic coordinates, velocities, box size, thermostat momenta, and barostat momenta is also written out.

Bottom Line: 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.WIREs Comput Mol Sci 2015, 5:310-323. doi: 10.1002/wcms.1220.

View Article: PubMed Central - PubMed

Affiliation: Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science Kobe, Japan.

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.

No MeSH data available.


Related in: MedlinePlus