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 cornparison, 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.