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.

Acceleration of molecular dynamics simulation of multiphase systems on GPU

2012 ◽  
Vol 9 (2) ◽  
pp. 76-79
Author(s):  
D.F. Marin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Intermolecular Interaction ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Lennard Jones ◽  
Multiphase Systems ◽  
And Performance ◽  
Dynamics Simulations

The paper presents results on acceleration of molecular dynamics simulations with the usage of GPUs. A system of water molecules is considered as an example of polar liquid. The intermolecular interaction is modeled with the usage of Coulomb and truncated Lennard-Jones potentials. Results of computational experiments on acceleration and performance of the developed code are presented.

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.

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.

scholarly journals Molecular dynamics simulation of soot formation during diesel combustion with oxygenated fuel addition

2020 ◽  
Vol 22 (36) ◽  
pp. 20829-20836
Author(s):  
Cheng Chen ◽  
Xi Jiang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Constant Temperature ◽  
Soot Formation ◽  
Dynamics Simulation ◽  
Diesel Combustion ◽  
Oxygenated Additives ◽  
Oxygenated Fuel

The morphology of nascent soot and the effect of oxygenated additives on sooting mitigation at a constant temperature of 3000 K.

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.

THE "FOLDING" BEHAVIORS OF HOMOPOLYMERS WITH ONE END FIXED

2004 ◽  
Vol 18 (15) ◽  
pp. 2123-2139 ◽  
Author(s):  
BIN XUE ◽  
JUN WANG ◽  
WEI WANG
Keyword(s):  
Molecular Dynamics ◽  
Chain Length ◽  
Conformational Changes ◽  
Canonical Ensemble ◽  
Interaction Strength ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Native Conformation ◽  
Collapse Temperature

We study the "folding" behaviors of homopolymers with one end fixed. By using canonical ensemble molecular dynamics simulation method, we observe the conformational changes during folding processes. Long chains collapse to the helical nuclei, then regroup to helix from the free-end to form the compact conformations through the middle stages of helix-like coil and helix-like cone, while short chains do not apparently have the above mentioned middle stages. Through simulated annealing, the native conformation of homopolymer chain in our model is found to be helix. We show the relations between specific heat C v (T) and radius of gyration R g (T) as functions of temperature, chain length and the interaction strength, respectively. We find that these two quantities match well and can be combined to interpret the "folding" process of the homopolymer. It is found that the collapse temperature Tθ and the native-like folding temperature T f do not change with the chain length in our model, however the interaction strength affects the values of Tθ and T f .

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