xianghong qi wrote:
Hi, Mark,

Which method can work with exclusion? Could you give me some hints for that? Thanks again.

I'm not your free teacher... :-) You need to have a much better working knowledge of MD than one such that you need to ask that question. Certainly with your present knowledge, it seems you should not be attempting some study where you're turning off some interactions for some unknown purpose. The first few chapters of the GROMACS manual are a great place to start, and you won't get anywhere without them.

Mark
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