complexity and convergence of electrostatic and van der waals energies within pme and cutoff methods复杂性和收敛的静电和范德瓦耳斯能量在中外和截止方法.pdfVIP

Int. J. Mol. Sci. 2004, 5, 154-173 International Journal of Molecular Sciences ISSN 1422-0067 © 2004 by MDPI /ijms/ Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods 1 1 2 Radka Svobodová Vařeková , Jaroslav Koča * and Chang-Guo Zhan * 1 National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic 2Division of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 907 Rose Street, Room 501B, Lexington, KY 40536, USA Tel.: +420 541 129 593, Fax: + 420 541 129 506, E-mail: jkoca@chemi.muni.cz URL: http://www.chemi.muni.cz/~jkoca * Author to whom correspondence should be addressed. Received: 15 December 2003 / Accepted: 11 March 2004 / Published: 01 April 2004 Abstract: In this paper, we report a detailed comparison between the popularly used cutoff and Particle Mesh Ewald (PME) methods in terms of the time complexity and the energy convergence of the long-range electrostatic and van der Waals interaction calculations. For the comparison, we performed various calculations on various representative biological molecules, including seven peptides and proteins, eleven oligonucleotides, and three conformations of a nucleotide-sugar. The results provide useful insights into the appropriate choice of the methods