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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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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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fig04: 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.

Mentions: In all simulations, the lipid bilayers maintained structural integrity, that is, there was no collapse in the bilayer structure, even at high temperature and under high surface tension. The acceptance ratio for the Metropolis criteria in all REMD simulations was about 0.3 in temperature space and 0.4 in surface-tension space, indicating frequent parameter exchanges between pairs of replicas. Figure 4(a) shows snapshots obtained from the MD and T-REMD simulations at T = 303.15 K. In T-REMD, the two lipid components are mixed more compared to MD, simply because high temperature accelerates lipid lateral diffusion. We analysed the mean-square displacement (MSD) of the centre of mass of lipid to examine lipid lateral diffusion (Figure 4(b)). All REMD simulations showed accelerated diffusion, where T-REMD was the most efficient and the order was T-REMD > γT-REMD > γ-REMD > MD. The enhanced lipid lateral diffusion observed in γ-REMD is due to free-area effects.52,95 Note that diffusion and mixing are not identical in the lipid-bilayer systems. To quantify the degree of mixing of two lipid components, we analysed the number of contact pairs between POPC and DMPC. Contact pairs were defined based on the distance between the centres of mass of lipids with a cutoff distance of 10 Å. Figure 4(c) shows a histogram of the number of contact pairs obtained from the snapshots at T = 303.15 K and γ = 0 dyn/cm after 10 ns. We found that the mixing of the two components was enhanced in T-REMD compared to MD, while it was suppressed in γ-REMD. In γT-REMD, both enhancement and suppression were observed, presumably because diffusion is accelerated at high temperature while it is suppressed under high surface tension. There is a controversy about the effects of membrane tension on the phase formation in mixed lipid bilayers. Some studies suggest that membrane tension induces phase separation,96–99 while others suggest mixing100–102 or transition to other phases103 would result. Our observation that γ-REMD and γT-REMD suppresses mixing agrees with the former studies. We suggest that REMD methods are useful for exploring structures at phase boundaries in mixed lipid bilayer systems.


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)

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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Related In: Results  -  Collection

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Show All Figures
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fig04: 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.
Mentions: In all simulations, the lipid bilayers maintained structural integrity, that is, there was no collapse in the bilayer structure, even at high temperature and under high surface tension. The acceptance ratio for the Metropolis criteria in all REMD simulations was about 0.3 in temperature space and 0.4 in surface-tension space, indicating frequent parameter exchanges between pairs of replicas. Figure 4(a) shows snapshots obtained from the MD and T-REMD simulations at T = 303.15 K. In T-REMD, the two lipid components are mixed more compared to MD, simply because high temperature accelerates lipid lateral diffusion. We analysed the mean-square displacement (MSD) of the centre of mass of lipid to examine lipid lateral diffusion (Figure 4(b)). All REMD simulations showed accelerated diffusion, where T-REMD was the most efficient and the order was T-REMD > γT-REMD > γ-REMD > MD. The enhanced lipid lateral diffusion observed in γ-REMD is due to free-area effects.52,95 Note that diffusion and mixing are not identical in the lipid-bilayer systems. To quantify the degree of mixing of two lipid components, we analysed the number of contact pairs between POPC and DMPC. Contact pairs were defined based on the distance between the centres of mass of lipids with a cutoff distance of 10 Å. Figure 4(c) shows a histogram of the number of contact pairs obtained from the snapshots at T = 303.15 K and γ = 0 dyn/cm after 10 ns. We found that the mixing of the two components was enhanced in T-REMD compared to MD, while it was suppressed in γ-REMD. In γT-REMD, both enhancement and suppression were observed, presumably because diffusion is accelerated at high temperature while it is suppressed under high surface tension. There is a controversy about the effects of membrane tension on the phase formation in mixed lipid bilayers. Some studies suggest that membrane tension induces phase separation,96–99 while others suggest mixing100–102 or transition to other phases103 would result. Our observation that γ-REMD and γT-REMD suppresses mixing agrees with the former studies. We suggest that REMD methods are useful for exploring structures at phase boundaries in mixed lipid bilayer systems.

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