作者
Darrin M York, Tom A Darden, Lee G Pedersen
发表日期
1993/11/15
期刊
The Journal of chemical physics
卷号
99
期号
10
页码范围
8345-8348
出版商
AIP Publishing
简介
Simulations of the HIV-l protease unit cell using a 9 A cutoff, 9/18 A" 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 A simulation did not converge in 300 ps. Inclusion of a 9/18 A" 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 aI., J. Chern. Phys. 98, 10 089 (1993)], and illustrates the importance of including long-range electrostatic forces in large macromolecular systems.
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