Abstract
Simulations of the HIV-1 protease unit cell using a 9 Å cutoff, 9/18 Å ‘‘twin-range’’ cutoff, and full Ewald sums have been carried out to 300 ps. The results indicate that long-range electrostatic interactions are essential for proper representation of the HIV-1 protease crystal structure. The 9 Å simulation did not converge in 300 ps. Inclusion of a 9/18 Å ‘‘twin-range’’ cutoff showed significant improvement. Simulation using the Ewald summation convention gave the best overall agreement with x-ray crystallographic data, and showed the least internal differences in the time average structures of the asymmetric units. The Ewald simulation represents an efficient implementation of the Particle Mesh Ewald method [Darden et al., J. Chem. Phys. 98, 10 089 (1993)], and illustrates the importance of including long-range electrostatic forces in large macromolecular systems.
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