GPU Computing in Biomolecular Modeling and Nanodesign

  • Tibor Kožár
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7125)


In addition to the intended use of graphics processing units (GPU) to accelerate computer games, their potential has become apparent for scientific computations in the recent years. Molecular modeling and molecular design are only few examples of numerous research areas that are significantly benefiting from novel developments of hardware and software platforms. For example, the impact of high computational power of GPUs has been demonstrated in molecular dynamics (MD) simulations or quantum chemical (QC) calculations. Thus far, several MD programs have been adapted to GPU computing, including NAMD/VMD, GROMACS, AMBER, etc. In addition, modeling tools intended for molecular design based on receptor-ligand interactions, such as molecular docking or core hopping protocols have recently been updated for GPU environment. The tremendous increase in the computing power facilitated by the integration of GPUs and the availability of GPU-based systems could accelerate material research on nanoscale. The price/performance ratio of GPU-based systems supports the development of custom-made protocols for efficient modeling of biomolecular systems and nanostructures. GPU-related molecular modeling tools will also accelerate the combined quantum chemical/molecular mechanics (QC/MM) methodologies. An overview of the performance of NVIDIA Tesla GPU-based system built for high-performance and high-throughput computing aimed for biomolecular modeling and nanodesign is presented.


GPU computing molecular modeling molecular dynamics simulations 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Tibor Kožár
    • 1
  1. 1.Department of Biophysics, Institute of Experimental PhysicsSlovak Academy of SciencesKošiceSlovakia

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