Performance Analysis Cluster Computing Environments on Molecular Dynamic Simulation of RAD GTPase and LOXCurcumin Molecules with AMBER
Implementation of virtual laboratory on scientific research has produced huge acceleration. One of the virtual scientific research activity is molecular dynamic simulation. The virtual experiments need high computing resources to solve the problem. AMBER is one of the software that provides molecular dynamic simulation that can utilize the parallel computing facilities. In this paper, we conduct the molecular dynamic experiments in order to know reliability of cluster computing environment. The results show that an implicit solvent simulation takes longer time than that in vacuum scenario since one has to consider existence of solvent surround the molecules so the computation is much longer than in vacuum; that the speed up will likely to remain constant on certain additional number of processors; and that there is no significant speed up for case in the LOX-Curcumin explicit solvent simulation.
Keywords: Performance Analysis, Molecular Dynamic, Cluster Computing, AMBER.
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ABOUT THE AUTHORS
Heru Suhartanto
Heru Suhartanto is a Professor in Faculty of Computer Science, Universitas Indonesia (Fasilkom UI). He has been with Fasilkom UI since 1986. Previously he held some positions such as Post doctoral fellow at Advanced Computational Modelling Centre, the University of Queensland, Australia in 1998 – 2000; two periods vice Dean for General Affair at Fasilkom UI since 2000. He graduated from undergraduate study at Department of Mathematics, UI in 1986. He holds Master of Science, from Department of Computer Science, The University of Toronto, Canada since 1990. He also holds Ph.D in Parallel Computing from Department of Mathematics, The University of Queensland since 1998. His main research interests are Numerical, Parallel, Cloud and Grid computing. He is also a member of reviewer of several referred international journal such as journal of Computational and Applied Mathematics, International Journal of Computer Mathematics, and Journal of Universal Computer Science. Furthermore, he has supervised some Master and PhD students; he has won some research grants; holds several software copyrights; published a number of books in Indonesian and international papers in proceeding and journal. He is also member of IEEE and ACM.
Arry Yanuar
Arry Yanuar is an assistant Professor in Faculty of Pharmacy, Universitas Indonesia since 1990. He graduated from undergraduate program Department of Pharmacy, Universitas Indonesia in 1990. He also holds Pharmacist Profession certificate in 1991. In 1997, he finished his Master Program from Department of Pharmacy, Universitas Gadjah Mada. He holds PhD in 2006 from Nara Institute of Science and Technology (NAIST), Jepang, with Structure Biology/protein Cristalography laboratorium. In 1999-2003 he worked as pharmacy expert in ISO certification for pharmacy industries at Llyod Register Quality Assurance. In 2002, he visited National Institute of Health (NIH), Bethesda, USA. He won several research grants and published some paper at international journals and conferences.
M. H. Hilman
Muhammad Hilman is a research Assistant at Faculty of Computer Science Universitas Indonesia (Fasilkom UI). He graduated from undergraduate and master program Fasilkom UI.
Ari Wibisono
Ari Wibisono is a research Assistant at Faculty of Computer Science Universitas Indonesia (Fasilkom UI). He graduated from undergraduate and master program Fasilkom UI.
Toni Dermawan
Toni Dermawan is a research Assistant at Faculty of Computer Science Universitas Indonesia (Fasilkom UI). He graduated from undergraduate Fasilkom UI.
Heru Suhartanto
Heru Suhartanto is a Professor in Faculty of Computer Science, Universitas Indonesia (Fasilkom UI). He has been with Fasilkom UI since 1986. Previously he held some positions such as Post doctoral fellow at Advanced Computational Modelling Centre, the University of Queensland, Australia in 1998 – 2000; two periods vice Dean for General Affair at Fasilkom UI since 2000. He graduated from undergraduate study at Department of Mathematics, UI in 1986. He holds Master of Science, from Department of Computer Science, The University of Toronto, Canada since 1990. He also holds Ph.D in Parallel Computing from Department of Mathematics, The University of Queensland since 1998. His main research interests are Numerical, Parallel, Cloud and Grid computing. He is also a member of reviewer of several referred international journal such as journal of Computational and Applied Mathematics, International Journal of Computer Mathematics, and Journal of Universal Computer Science. Furthermore, he has supervised some Master and PhD students; he has won some research grants; holds several software copyrights; published a number of books in Indonesian and international papers in proceeding and journal. He is also member of IEEE and ACM.
Arry Yanuar
Arry Yanuar is an assistant Professor in Faculty of Pharmacy, Universitas Indonesia since 1990. He graduated from undergraduate program Department of Pharmacy, Universitas Indonesia in 1990. He also holds Pharmacist Profession certificate in 1991. In 1997, he finished his Master Program from Department of Pharmacy, Universitas Gadjah Mada. He holds PhD in 2006 from Nara Institute of Science and Technology (NAIST), Jepang, with Structure Biology/protein Cristalography laboratorium. In 1999-2003 he worked as pharmacy expert in ISO certification for pharmacy industries at Llyod Register Quality Assurance. In 2002, he visited National Institute of Health (NIH), Bethesda, USA. He won several research grants and published some paper at international journals and conferences.
M. H. Hilman
Muhammad Hilman is a research Assistant at Faculty of Computer Science Universitas Indonesia (Fasilkom UI). He graduated from undergraduate and master program Fasilkom UI.
Ari Wibisono
Ari Wibisono is a research Assistant at Faculty of Computer Science Universitas Indonesia (Fasilkom UI). He graduated from undergraduate and master program Fasilkom UI.
Toni Dermawan
Toni Dermawan is a research Assistant at Faculty of Computer Science Universitas Indonesia (Fasilkom UI). He graduated from undergraduate Fasilkom UI.
