Accelerated RMSD Calculation for Molecular Metadynamics

@inproceedings{1360278,
   author = {Filipovič, Jiří and Pazúriková, Jana and Křenek, Aleš and Spiwok, Vojtěch},
   address = {Ghent, Belgie},
   booktitle = {Proceedings of the 2016 European Simulation and Modelling Conference},
   editor = {José Évora-Gómez and José Juan Hernandéz-Cabrera},
   keywords = {molecular metadynamics; RMSD; GPU acceleration},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {Ghent, Belgie},
   isbn = {978-90-77381-95-3},
   pages = {278-280},
   publisher = {EUROSIS - ETI},
   title = {Accelerated RMSD Calculation for Molecular Metadynamics},
   year = {2016}
}

TY  - JOUR
ID  - 1360278
AU  - Filipovič, Jiří - Pazúriková, Jana - Křenek, Aleš - Spiwok, Vojtěch
PY  - 2016
TI  - Accelerated RMSD Calculation for Molecular Metadynamics
PB  - EUROSIS - ETI
CY  - Ghent, Belgie
SN  - 9789077381953
KW  - molecular metadynamics
KW  - RMSD
KW  - GPU acceleration
N2  - In this paper, we introduce GPU acceleration of RMSD approximation, which is computationally demanding task in molecular metadynamics. Comparing to tuned CPU implementation, we have reached 4.4x speedup using mid-end GPU. The scaling of our GPU implementation is sufficient to be usable in real-world application.
ER  - 

FILIPOVIČ, Jiří, Jana PAZÚRIKOVÁ, Aleš KŘENEK a Vojtěch SPIWOK. Accelerated RMSD Calculation for Molecular Metadynamics. In José Évora-Gómez and José Juan Hernandéz-Cabrera. \textit{Proceedings of the 2016 European Simulation and Modelling Conference}. Ghent, Belgie: EUROSIS - ETI, 2016, s.~278-280. ISBN~978-90-77381-95-3.