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[求助] 求教怎样实现文献所说的预组装

The rods were constructed from 20 round slices placed along the z-direcction with 16 surfactant molecules per slice. Every second slice was rotated to make the surface of the rod more uniform.However, the rods has a hole inside ,due to the spatial structure  of individual molecules. In order to avoid occupation of the hole by water and to provide a resonable initial density of the hydrophobic core, the rods were shrunk in x- and y- dimensions.This was done in series of steps followed by geometry optimization to relax streched bonds.
请问文献里这个预组装成杆状还有shrunk progress具体怎样实现的?用什么软件呢?谢谢
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