Abstract
Cloud computing has emerged as a prevalent computing paradigm with the advantages of virtualization, scalability, fault tolerance, and a usage-based pricing model. It has been widely used in various computational research fields. Replica exchange molecular dynamics (REMD) and replica exchange statistical temperature molecular dynamics (RESTMD) are two sampling algorithms in molecular dynamics. Due to the inherent parallel feature of REMD and RESTMD, it is practical to convert them into cloud computing applications. However, the performance of REMD and RESTMD on clouds has not been extensively investigated. In our work, we implemented REMD and RESTMD in cloud computing environment through Hadoop, an open-source implementation of MapReduce platform, and evaluated the performance of REMD and RESTMD in cloud computing environment and in high performance computing (HPC) environment as reference. In our research, REMD and RESTMD exhibits good feasibility in cloud computing. Otherwise, cloud computing demonstrates the characteristics of virtualization, elasticity, and scalability, providing a robust environment for REMD and RESTMD. © 2013 IEEE.
Recommended Citation
J. Niu et al., "A Hadoop Approach To Advanced Sampling Algorithms In Molecular Dynamics Simulation On Cloud Computing," Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013, pp. 452 - 455, article no. 6732534, Institute of Electrical and Electronics Engineers, Dec 2013.
The definitive version is available at https://doi.org/10.1109/BIBM.2013.6732534
Department(s)
Computer Science
Keywords and Phrases
Cloud computing; Hadoop; REMD; RESTMD
International Standard Book Number (ISBN)
978-147991309-1
Document Type
Article - Conference proceedings
Document Version
Citation
File Type
text
Language(s)
English
Rights
© 2024 Institute of Electrical and Electronics Engineers, All rights reserved.
Publication Date
01 Dec 2013
