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Empirical valance bond method to hybrid multiple PES

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EVB

EVB的简单实现。MD engine使用OpenMM。其中OpenMM对AMOEBA的stretch bend force支持有个小bug,希望他们下一版改了吧……

用法:

  1. 制作用于描述体系拓扑的Tinker xyz文件和key文件。流程看这里:https://sites.google.com/site/amoebaworkshop/exercise-2
  2. 使用key2xml.py将上述文件转化为pdb文件和xml描述文件,作为EVB Halmitonian的对角项。
  3. 编辑conf.json,描述非对角项CV和所需常数。(示例文件施工中)
  4. 调用evb.py中的EVBHalmitonian类,将conf.json作为字典项传入,进行初始化。

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