GPU Acceleration of High-Speed Collision Molecular Dynamics Simulation

2009 ◽  
Author(s):  
Canqun Yang ◽  
Qiang Wu ◽  
Juan Chen ◽  
Zhen Ge
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
High Speed ◽  
Dynamics Simulation ◽  
Gpu Acceleration ◽  
High Speed Collision

scholarly journals Molecular dynamics simulation of high-speed loading of 2D boron nitride

2021 ◽  
Vol 11 (1) ◽  
pp. 79-83
Author(s):  
Igor Shepelev ◽  
Sergey Dmitriev ◽  
Elena Korznikova
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Boron Nitride ◽  
High Speed ◽  
Dynamics Simulation

Molecular dynamics simulation of the behavior of titanium under high-speed deformation

2021 ◽  
Author(s):  
Ivan V Nelasov ◽  
Andrey I. Kartamyshev ◽  
Anton Boev ◽  
Alexey Gennadievich Lipnitskii ◽  
Yury R. Kolobov ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
High Speed ◽  
Dynamics Simulation ◽  
High Speed Deformation

scholarly journals A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors

2014 ◽  
Vol 169 ◽  
pp. 63-87 ◽  
Author(s):  
David R. Glowacki ◽  
Michael O'Connor ◽  
Gaetano Calabró ◽  
James Price ◽  
Philip Tew ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Physics Education ◽  
Computational Simulation ◽  
Rare Event ◽  
Dynamics Simulation ◽  
Gpu Acceleration ◽  
Human Form ◽  
Depth Sensors ◽  
Water Solvent

With advances in computational power, the rapidly growing role of computational/simulation methodologies in the physical sciences, and the development of new human–computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone the motion of the simulated atoms, affecting both graphics and sonified simulation data. GPU acceleration has been key to achieving our target of 60 frames per second (FPS), giving an extremely fluid interactive experience. GPU acceleration has also allowed us to scale the system for use in immersive 360° spaces with an array of up to ten depth sensors, allowing several users to simultaneously chaperone the dynamics. The flexibility of our platform for carrying out molecular dynamics simulations has been considerably enhanced by wrappers that facilitate fast communication with a portable selection of GPU-accelerated molecular force evaluation routines. In this paper, we describe a 360° atmospheric molecular dynamics simulation we have run in a chemistry/physics education context. We also describe initial tests in which users have been able to chaperone the dynamics of 10-alanine peptide embedded in an explicit water solvent. Using this system, both expert and novice users have been able to accelerate peptide rare event dynamics by 3–4 orders of magnitude.

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