| Electrostatic interaction ant its energy: We did 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. Electronegativity equalization methods (EEM) for calculation of atomic charge: These methods (based on DFT) are an alternative to calculation of charge using ab initio methods. These methods are significantly faster than ab initio methods and their accurateness corresponds to ab initio methods (base STO-3G, Mullican population analysis). We implemented two methods: classical EEM and its extension ABEEM (atom-bond EEM). Then we tested our implementation, optimize created software and parallelize it. By optimization and parallelization we get markedly more effective code. We plan to use this software for calculation of conformationaly dependent charges in molecular dynamics. |
