General atomic and molecular electronic structure system
Journal of Computational Chemistry
General purpose molecular dynamics simulations fully implemented on graphics processing units
Journal of Computational Physics
Scalable Parallel Programming with CUDA
Queue - GPU Computing
GPU acceleration of cutoff pair potentials for molecular modeling applications
Proceedings of the 5th conference on Computing frontiers
Probing biomolecular machines with graphics processors
Communications of the ACM - A View of Parallel Computing
Probing Biomolecular Machines with Graphics Processors
Queue - Bioscience
Proceedings of the International Conference and Workshop on Emerging Trends in Technology
Journal of Computational Physics
Immersive out-of-core visualization of large-size and long-timescale molecular dynamics trajectories
ISVC'11 Proceedings of the 7th international conference on Advances in visual computing - Volume Part II
Introducing scalable quantum approaches in language representation
QI'11 Proceedings of the 5th international conference on Quantum interaction
Power and Performance Management of GPUs Based Cluster
International Journal of Cloud Applications and Computing
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The visualization of molecular orbitals (MOs) is important for analyzing the results of quantum chemistry simulations. The functions describing the MOs are computed on a three-dimensional lattice, and the resulting data can then be used for plotting isocontours or isosurfaces for visualization as well as for other types of analyses. Existing software packages that render MOs perform calculations on the CPU and require runtimes of tens to hundreds of seconds depending on the complexity of the molecular system. We present novel data-parallel algorithms for computing lattices of MOs on modern graphics processing units (GPUs) and multi-core CPUs. The fastest GPU algorithm achieves up to a 125-fold speedup over an optimized CPU implementation running on one CPU core. We also demonstrate possible benefits of dynamic GPU kernel generation and just-in-time compilation for MO calculation. We have implemented these algorithms within the popular molecular visualization program VMD, which can now produce high quality MO renderings for large systems in less than a second, and achieves the first-ever interactive animations of quantum chemistry simulation trajectories using only on-the-fly calculation.