Research PapersNo Access
Interaction sorting method for molecular dynamics on multi-core SIMD CPU architecture
Abstract
Molecular dynamics (MD) is widely used in computational biology for studying binding mechanisms of molecules, molecular transport, conformational transitions, protein folding, etc. The method is computationally expensive; thus, the demand for the development of novel, much more efficient algorithms is still high. Therefore, the new algorithm designed in 2007 and called interaction sorting (IS) clearly attracted interest, as it outperformed the most efficient MD algorithms. In this work, a new IS modification is proposed which allows the algorithm to utilize SIMD processor instructions. This paper shows that the improvement provides an additional gain in performance, 9% to 45% in comparison to the original IS method.
References
- Proc. Natl. Acad. Sci 99(20), 12777 (2002). Crossref, Medline, Google Scholar
- Proc. Natl. Acad. Sci 100(24), 13934 (2003). Crossref, Medline, Google Scholar
- Structure 14(3), 437 (2003). Crossref, Google Scholar
- Curr. Opin. Drug. Discov. Devel. 11(4), 559 (2008). Medline, Google Scholar
- Journal of Computational Chemistry 28(2), 570 (2007). Crossref, Medline, Google Scholar
S. Olivier , Porting the gromacs molecular dynamics code to the cell processor, Parallel and Distributed Processing Symposium (2007) pp. 1–8. Google Scholar- J. Amer. Chem. Soc. 58(1), 1486 (1936). Crossref, Google Scholar
- J. Chem. Phys. 119(1), 11556 (2003). Crossref, Google Scholar
- J. Chem. Phys. 110(1), 8254 (1999). Crossref, Google Scholar
- J. Chem. Phys. 134(1), 164107 (2011). Crossref, Medline, Google Scholar
- Biophys. Rev. 4(1), 161 (2012). Crossref, Medline, Google Scholar
- Comput. Phys. Commun. 119(1), 135 (1999). Crossref, Google Scholar
- Comput. Phys. Commun. 182(3), 611 (2011). Crossref, Google Scholar
- J. Comput. Chem. 32(7), 1386 (2011). Crossref, Medline, Google Scholar
- Numer. Meth. Programm. 11 , 299 ( 2010 ) . Google Scholar
- Intel®Manycore Testing Lab. http://software.intel.com/en-us/intel-manycore-testing-lab, Accessed 30 April 2014 . Google Scholar
- J. Comput. Phys. 13(3), 430 (1973). Crossref, Google Scholar
- Phys. Rev. 159(1), 98 (1967). Crossref, Google Scholar
- Chin. Sci. Bullet. 54(9), 1463 (2009). Crossref, Google Scholar
- J. Comput. Biol. 13(5), 1041 (2006). Crossref, Medline, Google Scholar
- Comput. Phys. Commun. 161(1), 27 (2004). Crossref, Google Scholar
- J. Comput. Chem. 33(1), 76 (2012). Crossref, Medline, Google Scholar
- The. J. Chem. Phys. 126 , 121102 ( 2007 ) . Crossref, Medline, Google Scholar
- Molecular. Simul. 39(9), 1 (2013). Crossref, Google Scholar
-
D. E. Knuth , The Art of Computer Programming ,Sorting and Searching 3 ( Addison-Wesley , Reading, MA , 1973 ) . Google Scholar - Proc. VLDB. Endowment. 1(2), 1313 (2008). Crossref, Google Scholar
- IEEE. Trans. Comput. 38(11), 1526 (1989). Crossref, Google Scholar
- Commun. ACM. 29(12), 1170 (1986). Crossref, Google Scholar
- Biophysics 51(1), 110 (2006). Crossref, Google Scholar
- Hybrid supercomputing cluster NKS-30T+GPU. http://www2.sscc.ru/HKC-30T/HKC-30T.htm. Accessed 30 April 2014 . Google Scholar
Published: 9 January 2015
