I meet a problem in run MD: from the display of VMD, there are some H-H bonds formed during the MD. All the bonds I wrote in .itp file are right, except these new unexpected H-H bonds. (I generate the system from a smaller system, EM is ok, when running NTV, the problem comes. ) Who can give some suggestions? Thanks in advances.
PS: I have succeeded in simulating a samller system by using the same force-field. So I think the .itp file should be right.
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Sincerely yours,
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Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
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