On 7/11/2010 9:36 PM, leila karami wrote:
Dear Mark thanks for your attention. I read manual before. I know that g_hbond is for hydrogen bond analysis. But I don’t know about Van der Waals interactions analysis and how to obtain percentage of them.
If you're planning to copy someone else's analysis, then you should be able to do so from their description. That's why they wrote the paper... If they don't make a description, either email them to ask, or choose someone else to copy :-). Unfortunately, "van der Waals interactions analysis" is far too vague to be a useful target question. As your email pointed out, there's a bunch of mathematical parameters that go into assigning hydrogen bonds for any analysis there... Something similar would have to apply to vdW, and the procedure for finding that out will often lead you towards a good method for implementing it.
Mark
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