10676
You-Liang Zhu, Hong Liu, Zhan-Wei Li, Hu-Jun Qian, Giuseppe Milano, Zhong-Yuan Lu
A new molecular simulation toolkit composed of some lately developed force fields and specified models is presented to study the self-assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by utilizing the computational power of GPUs. In addition, the hierarchical self-assembly of soft anisotropic particles and the problems related to polymerization can […]
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Nikesh S. Dattani
This MATLAB program calculates the dynamics of the reduced density matrix of an open quantum system modeled by the Feynman-Vernon model. The user gives the program a vector describing the coordinate of an open quantum system, a hamiltonian matrix describing its energy, and a spectral distribution function and temperature describing the environment’s influence on it, […]
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Rio Yokota, Jaydeep P. Bardhan, Matthew G. Knepley, L. A. Barba, Tsuyoshi Hamada
We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a boundary element method (BEM) formulation of the continuum electrostatic model, as well as the BIBEE approximation to BEM. The hardware acceleration is achieved through […]
A. Zhmurov, K. Rybnikov, Y. Kholodov, V. Barsegov
The use of graphics processing units (GPUs) in simulation applications offers a significant speed gain as compared to computations on central processing units (CPUs). Many simulation methods require a large number of independent random variables generated at each step. We present two approaches for implementation of random number generators (RNGs) on a GPU. In the […]
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A. Zhmurov, K. Rybnikov, Y. Kholodov, V. Barsegov
Langevin Dynamics, Monte Carlo, and all-atom Molecular Dynamics simulations in implicit solvent, widely used to access the microscopic transitions in biomolecules, require a reliable source of random numbers. Here we present the two main approaches for implementation of random number generators (RNGs) on a GPU, which enable one to generate random numbers on the fly. […]
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Free GPU computing nodes at hgpu.org

Registered users can now run their OpenCL application at hgpu.org. We provide 1 minute of computer time per each run on two nodes with two AMD and one nVidia graphics processing units, correspondingly. There are no restrictions on the number of starts.

The platforms are

Node 1
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  • GPU device 1: AMD/ATI Radeon HD 6970 2GB, 880MHz
  • CPU: AMD Phenom II X6 @ 2.8GHz 1055T
  • RAM: 12GB
  • OS: OpenSUSE 13.1
  • SDK: AMD APP SDK 2.9
Node 2
  • GPU device 0: AMD/ATI Radeon HD 7970 3GB, 1000MHz
  • GPU device 1: nVidia GeForce GTX 560 Ti 2GB, 822MHz
  • CPU: Intel Core i7-2600 @ 3.4GHz
  • RAM: 16GB
  • OS: OpenSUSE 12.2
  • SDK: nVidia CUDA Toolkit 6.0.1, AMD APP SDK 2.9

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