Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods

International Journal of Molecular Sciences

Radka Svobodová Vaᖞková¹  Jaroslav Koლ¹ 

[1] National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic

关键词: Van der Waals energy;    electrostatic energy;    convergence of energy;    PME;    cutoff method;   

DOI  :  10.3390/i5040154

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
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