Can anyone help me with how to analyze the effecting of hydrogen bonds?

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Daniel R Roe

You may want to try the 'hbond' command in Cpptraj, freely available with AmberTools 14 (http://ambermd.org/AmberTools14-get.html). Cpptraj supports many popular MD trajectory formats.

Ibrahim A Osman

Thanx alot dear # Luca Belmonte # Daniel R Roe for great answers but already i did the commands and measuring hydrogen bonds but my question about how to analyse if can guide me with a good references