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Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods
National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
Division of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 907 Rose Street, Room 501B, Lexington, KY 40536, USA
* Authors to whom correspondence should be addressed.
Received: 15 December 2003; Accepted: 11 March 2004 / Published: 1 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 (i.e. the cutoff or PME) and that of the cutoff values for the calculations on different kinds of molecules. It has also been demonstrated that for some cases using different cutoff values for calculating the electrostatic and van der Waals interaction energies will be computationally more efficient.
Keywords: Van der Waals energy; electrostatic energy; convergence of energy; PME; cutoff method
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Vařeková, R.S.; Koča, J.; Zhang, C.-G. Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods. Int. J. Mol. Sci. 2004, 5, 154-173.
Vařeková RS, Koča J, Zhang C-G. Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods. International Journal of Molecular Sciences. 2004; 5(4):154-173.
Vařeková, Radka S.; Koča, Jaroslav; Zhang, Chang-Guo. 2004. "Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods." Int. J. Mol. Sci. 5, no. 4: 154-173.