Molecular modeling on GPUs
Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.
In 2007, NVIDIA introduced video cards that could be used not only to show graphics but also for scientific calculations. These cards include many arithmetic units (currently up to 240) working in parallel. Long before this event, the computational power of video cards was used to accelerate calculations. What was new is that NVIDIA made it possible to develop parallel programs in a high-level language. This technology (called CUDA) substantially simplified programming by introducing the CUDA code in programs written in на C/C++.
Quantum culculations [1] [2] [3] and, particularly, molecular mechanics simulations [4] [5] (molecular modeling in terms of classical mechanics) are among beneficial applications of this technology. The video cards can accelerate the calculations tens of times. Thus, a PC with such a card has the power similar to that of a cluster of workstations based on the common processors.
GPU accelerated software
- VMD & NAMD - Visual Molecular Dynamics
- HOOMD - Highly Optimized Object Oriented Molecular Dynamics
- Ascalaph molecular modelling suite
- GPUGRID distributed supercomputing infrastructure
- Folding@Home distributed computing project
See also
References
- ^ Koji Yasuda (2008). "Accelerating Density Functional Calculations with Graphics Processing Unit". J. Chem. Theory Comput. 4: 1230–1236.
- ^ Koji Yasuda (2007). "Two-electron integral evaluation on the graphics processor unit". Journal of Computational Chemistry. 29: 334–342.
- ^ Leslie Vogt, Roberto Olivares-Amaya, Sean Kermes, Yihan Shao, Carlos Amador-Bedolla and Alán Aspuru-Guzik (2008). "Accelerating Resolution-of-the-Identity Second-Order Møller−Plesset Quantum Chemistry Calculations with Graphical Processing Units". J. Phys. Chem. A. 112: 2049–2057.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Joshua A. Anderson, Chris D. Lorenz, A. Travesset (2008). "General Purpose Molecular Dynamics Simulations Fully Implemented on Graphics Processing Units". Journal of Computational Physics. 227: 5342–5359.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, and Wen-Mei W. Hwu. (2008). "GPU acceleration of cutoff pair potentials for molecular modeling applications". In CF'08: Proceedings of the 2008 conference on Computing frontiers, New York, NY, USA: 273–282.
{{cite journal}}: CS1 maint: multiple names: authors list (link)