Accelerated RMSD Calculation for Molecular Metadynamics
| Authors | |
|---|---|
| Year of publication | 2016 |
| Type | Article in Proceedings |
| Conference | Proceedings of the 2016 European Simulation and Modelling Conference |
| MU Faculty or unit | |
| Citation | FILIPOVIČ, Jiří; Jana PAZÚRIKOVÁ; Aleš KŘENEK and Vojtěch SPIWOK. Accelerated RMSD Calculation for Molecular Metadynamics. In José Évora-Gómez and José Juan Hernandéz-Cabrera. Proceedings of the 2016 European Simulation and Modelling Conference. Ghent, Belgie: EUROSIS - ETI, 2016, p. 278-280. ISBN 978-90-77381-95-3. |
| Field | Informatics |
| Keywords | molecular metadynamics; RMSD; GPU acceleration |
| Attached files | |
| Description | 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. |
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