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MD模拟中的盒子大小问题

已有 2660 次阅读 2018-6-29 23:03 |系统分类:科研笔记

 

The most important question to ask now is why choose 1.2 nm? The short answer is that you don't want the protein to 'see' its periodic image across the boundary of the box. If you refer to the original paper for the AMBER 03 force field (Duan, et al., J. Comput. Chem. 2003, 24, 1999-2012), they use short-range VDW and electrostatic cut-offs of 0.8 nm - when you begin simulating, it is very important to do the same. In order for the protein to avoid seeing its image across the periodic boundary, it must be at least twice the cut-off distance from the next nearest image of itself. That being said, the space between the protein and the edge of the box only really needs to be slightly larger than 0.8 nm, but it is still a good idea to include extra space especially if there is a chance the protein might unfold a little bit or if is an oblong shape. It is better to have a slightly larger box size now than to find out later that your protein was interacting with its periodic image during the simulation. (See the image below).

File:Pbc overlap.jpg

The dashed black squares indicate the box boundaries, and the dashed red circles indicate the short-range VDW and electrostatic  cut-offs. So long as the red circles do not overlap, the protein will not be able to "see" its periodic image.

灰色虚线代表盒子的边界,红色虚线代表短程范德华和静电作用截断值。因此只要红色圆圈不重叠,蛋白就不会看到自己的周期图像。因此当截断值设置为8埃时,盒子的大小d至少要大于8埃。

摘自http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water



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