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Hi Ran. If I understand you right, then you suggest to have one molecule as acceptor, and the rest (499) as donors, and then look in the hbnum.xvg to see how often there is two hydrogen bonds... 1. is that I have to do this check for every molecule. 2. there is no guaranty that the two hydrogen bonds are to the same other molecule - it could very well be as a part of a chain... 3. If possible I would like to do measurement of distance between molecules when they are bonded as a dimer... Best regards Rasmus Ran Friedman wrote: Hi Rasmus, A simple solution would be to run g_hbond twice, with two separate groups for acetate 1 as donor and acetate 2 as acceptor or vice versa, check the existence an hydrogen bond with g_hbond -num and write a script to check when the two hydrogen bonds co-exist.Hope that helps, Ran. Rasmus "Termo" Lundsgaard wrote: |
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