FMM/GPU Accelerated Molecular Dynamics Simulation of Phase Transitions in Water-Nitrogen-Metal Systems

2012 ◽  
Author(s):  
Elena Moiseeva ◽  
Constantin Mikhaylenko ◽  
Victor Malyshev ◽  
Dmitry Maryin ◽  
Nail Gumerov
Keyword(s):  
Molecular Dynamics ◽  
Graphics Processing Units ◽  
High Performance ◽  
Fast Multipole Method ◽  
Pure Water ◽  
Water Dynamics ◽  
Dynamics Simulation ◽  
Problem Size ◽  
Central Processing ◽  
Dynamics Simulations

To characterize the behavior of water with dissolved gas (nitrogen) near a solid metallic substrate, which is important for realistic modeling of flows in nanochannels, the method of molecular dynamics is used. High performance computing is achieved via the Fast Multipole Method (FMM) for the force evaluation and via utilization of heterogeneous architectures which consists of central processing units (CPUs) and graphics processing units (GPUs). The FMM allows one to speed up computations of the long-range interactions (Coulomb potential) due to the linear scaling of the algorithm with the problem size. Utilization of the GPU provides significant acceleration of computations. Realization of the FMM on GPUs allows one to perform computational experiments for very large systems. The paper shows that the described technique can be used for water dynamics simulations in a region of size up to 100 nanometers, or of the order 100 millions molecules on personal supercomputers equipped with several GPUs. Results of numerical experiments on structure formation on the contact interface of a water droplet and metal surface both for pure water and for water with dissolved air are reported.

scholarly journals Molecular dynamics simulation of the Pb(II) coordination in biological media via cationic dummy atom models

2021 ◽  
Vol 140 (2) ◽  
Author(s):  
Iogann Tolbatov ◽  
Alessandro Marrone
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Aqueous Solutions ◽  
Pure Water ◽  
Dynamics Simulation ◽  
Ligand Interaction ◽  
Amber Force Field ◽  
Dummy Atom ◽  
Dynamics Simulations ◽  
Potential Use

AbstractThe coordination of Pb(II) in aqueous solutions containing thiols is a pivotal topic to the understanding of the pollutant potential of this cation. Based on its hard/soft borderline nature, Pb(II) forms stable hydrated ions as well as stable complexes with the thiol groups of proteins. In this paper, the modeling of Pb(II) coordination via classical molecular dynamics simulations was investigated to assess the possible use of non-bonded potentials for the description of the metal–ligand interaction. In particular, this study aimed at testing the capability of cationic dummy atom schemes—in which part of the mass and charge of the Pb(II) is fractioned in three or four sites anchored to the metal center—in reproducing the correct coordination geometry and, also, in describing the hard/soft borderline character of this cation. Preliminary DFT calculations were used to design two topological schemes, PB3 and PB4, that were subsequently implemented in the Amber force field and employed in molecular dynamics simulation of either pure water or thiol/thiolate-containing aqueous solutions. The PB3 scheme was then tested to model the binding of Pb(II) to the lead-sensing protein pbrR. The potential use of CDA topological schemes in the modeling of Pb(II) coordination was here critically discussed.

scholarly journals High-throughput of measure-preserving integrators for constant temperature molecular dynamics simulations on GPUs

2018 ◽  
Author(s):  
Luis Guarneros-Nolasco ◽  
Ketzasmin A. Terrón-Mejía ◽  
Jorge Mulia-Rodríguez ◽  
Daniel Osorio-Gonzalez ◽  
Roberto López-Rendón ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Constant Temperature ◽  
High Throughput ◽  
Graphics Processing Units ◽  
Canonical Ensemble ◽  
Dynamics Simulation ◽  
Wide Range ◽  
And Performance ◽  
Dynamics Simulations ◽  
Reported Data

Molecular dynamics simulation is currently the theoretical technique eligible to simulate a wide range of systems from soft condensed matter to biological systems. However, of the excellent results that the technique has arrogated, this approach remains computationally expensive, but with the emergence of the new supercomputing technologies bases on graphics processing units graphical processing units-based systems GPUs, the perspective has changed. The GPUs allow performing large and complex simulations at a significantly reduced time. In this work, we present recent innovations in the acceleration of molecular dynamics in GPUs to simulate non-Hamiltonian systems. In particular, we show the performance of measure-preserving geometric integrator in the canonical ensemble, that is, at constant temperature. We provide a validation and performance evaluation of the code by calculating the thermodynamic properties of a Lennard-Jones fluid. Our results are in excellent agreement with reported data reported from literature, which were calculated with CPUs. The scope and limitations for performing simulations of high-throughput MD under rigorous statistical thermodynamics in the canonical ensemble are discussed and analyzed.

Large Scale Molecular Dynamics Simulations of a Liquid Crystalline Droplet with Fast Multipole Implementations

1998 ◽  
Vol 538 ◽  
Author(s):  
Zhiqiang Wang ◽  
James Lupo ◽  
Soumya S. Patnaik ◽  
Alan McKenney ◽  
Ruth Pachter
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Electrostatic Interactions ◽  
Liquid Crystalline ◽  
Fast Multipole Method ◽  
Atomic Scale ◽  
Dynamics Simulation ◽  
Fast Multipole ◽  
Multipole Method ◽  
Dynamics Simulations

AbstractThe Fast Multipole Method (FMM) offers an efficient way (order O(N)) to handle long range electrostatic interactions, thus enabling more realistic molecular dynamics simulations of large molecular systems. The performance of the fast molecular dynamics (FMD) code, a parallel MD code being developed in our group, using the three-dimensional fast multipole method, shows a good speedup. The application to the full atomic-scale molecular dynamics simulation of a liquid crystalline droplet of 4-n-pentyl-4'-cyanobiphenyl (5CB) molecules, of size 35,872 atoms, shows strong surface effects on various orientational order parameters.

scholarly journals Trehalose Stabilizing Protein in a Water Replacement Scenario: Insights from Molecular Dynamics Simulation

2019 ◽  
Author(s):  
Qiang Shao ◽  
Jinan Wang ◽  
Weiliang Zhu
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Pure Water ◽  
Dynamics Simulation ◽  
Mixed Solution ◽  
Water Replacement ◽  
Model Protein ◽  
Active Research ◽  
Dynamics Simulations ◽  
Water Hydrogen

AbstractHow trehalose has exceptional property in helping biomolecules preserve their native structures remains a subject of active research. Running molecular dynamics simulations on a model protein in low-concentrated trehalose solution and pure water, respectively, the present study verifies the ability of trehalose in stabilizing protein native structure and provides a comprehensive atomic-level picture of the molecular interactions among protein, trehalose, and water in their mixed solution. Trehalose directly interacts to and meanwhile affects the interactions between the other species via hydrogen bonding: 1) trehalose molecules are clustered through inter-molecular hydrogen bonding interaction; 2) trehalose forms hydrogen bond with water which influences the strength of water-water hydrogen bonding network but does not impair protein-water hydrogen bonding; 3) trehalose is accessible to form hydrogen bonds towards protein and simultaneously replace water molecules around protein which reduces the hydrogen bonding possibility from water to protein, in accordance with “water replacement” scenario.

scholarly journals Molecular dynamics simulation of ice growth from supercooled pure water and from salt solution

2006 ◽  
Vol 44 ◽  
pp. 113-117 ◽  
Author(s):  
M.A. Carignano ◽  
E. Baskaran ◽  
P.B. Shepson ◽  
I. Szleifer
Keyword(s):  
Molecular Dynamics ◽  
Metastable State ◽  
Salt Solution ◽  
Pure Water ◽  
Cluster Formation ◽  
Dynamics Simulation ◽  
Final State ◽  
Ice Growth ◽  
Dynamics Simulations ◽  
Salt Systems

AbstractThe kinetics of ice growth on the prismatic and basal planes is studied by molecular dynamics simulations. The time evolution of two systems has been investigated. In one a slab of ice is initially in contact with supercooled water, while in the second the ice is in contact with a supercooled salt solution. The simulations were done at a temperature below the eutectic temperature, and complete solidification is observed. The total freezing time is longer in the systems with ions than in the systems with pure water. The final state for the salt systems always shows the formation of ion clusters. For the ionic system growing on the prismatic plane, an intermediate metastable state is observed before total solidification. The duration of this metastable state depends on the ability of the system to get all the ions participating in cluster formation. The simulations enable understanding of the mechanisms for ice formation under different solution conditions.

Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

2011 ◽  
Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Transition Temperature ◽  
Peak Position ◽  
Temperature Curve ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Dynamics Simulations ◽  
First Time ◽  
Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

scholarly journals Reactive molecular dynamics simulation of the high-temperature pyrolysis of 2,2′,2′′,4,4′,4′′,6,6′,6′′-nonanitro-1,1′:3′,1′′-terphenyl (NONA)

RSC Advances ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 5507-5515
Author(s):  
Liang Song ◽  
Feng-Qi Zhao ◽  
Si-Yu Xu ◽  
Xue-Hai Ju
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Reactive Molecular Dynamics ◽  
Ring Compounds ◽  
Fused Ring ◽  
Dynamics Simulations

The bimolecular and fused ring compounds are found in the high-temperature pyrolysis of NONA using ReaxFF molecular dynamics simulations.

Molecular Dynamics Simulation Study of Lecithin Inhibiting Hydrate-Dissociation

2017 ◽  
Vol 890 ◽  
pp. 252-259
Author(s):  
Le Wang ◽  
Guan Cheng Jiang ◽  
Xin Lin ◽  
Xian Min Zhang ◽  
Qi Hui Jiang
Keyword(s):  
Molecular Dynamics ◽  
Water Movement ◽  
Simulation Analysis ◽  
Mass Density ◽  
Dynamics Simulation ◽  
Dissociation Process ◽  
Hydrate Dissociation ◽  
Hydrocarbon Chains ◽  
Dynamics Simulations ◽  
Mass Density Profile

Molecular dynamics simulations are used to study the dissociation inhibiting mechanism of lecithin for structure I hydrates. Adsorption characteristics of lecithin and PVP (poly (N-vinylpyrrolidine)) on the hydrate surfaces were performed in the NVT ensemble at temperatures of 277K and the hydrate dissociation process were simulated in the NPT ensemble at same temperature. The results show that hydrate surfaces with lecithin is more stable than the ones with PVP for the lower potential energy. The conformation of lecithin changes constantly after the balanced state is reached while the PVP molecular dose not. Lecithin molecule has interaction with lecithin nearby and hydrocarbon-chains of lecithin molecules will form a network to prevent the diffusion of water and methane molecules, which will narrow the available space for hydrate methane and water movement. Compared with PVP-hydrate simulation, analysis results (snapshots and mass density profile) of the dissociation simulations show that lecithin-hydrate dissociates more slowly.

Molecular Dynamics Simulations of High Energy Cascades in Iron

1994 ◽  
Vol 373 ◽  
Author(s):  
Roger E. Stoller
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
High Energy ◽  
Dynamics Simulation ◽  
Method Of Molecular Dynamics ◽  
Energy Cascades ◽  
Iron Based ◽  
The Many ◽  
Property Changes ◽  
Dynamics Simulations

AbstractA series of high-energy, up to 20 keV, displacement cascades in iron have been investigated for times up to 200 ps at 100 K using the method of molecular dynamics simulation. Thesimulations were carried out using the MOLDY code and a modified version of the many-bodyinteratomic potential developed by Finnis and Sinclair. The paper focuses on those results obtained at the highest energies, 10 and 20 keV. The results indicate that the fraction of the Frenkel pairs surviving in-cascade recombination remains fairly high in iron and that the fraction of the surviving point defects that cluster is lower than in materials such as copper. In particular, vacancy clustering appears to be inhibited in iron. Some of the interstitial clusters were observed to exhibit an unexpectedly complex, three-dimensional morphology. The observations are discussed in terms of their relevance to microstructural evolution and mechanical property changes in irradiated iron-based alloys.

Sign in / Sign up

Export Citation Format

Share Document