[gmx-users] How to evaluate the Hbond and non-bonded interactions between ligand-receptor

mmousivand93 mmousivand93 at ut.ac.ir
Sun Aug 26 18:03:38 CEST 2018

Dear all users 

Hi, I have run molecular dynamic for SSDNA-Ligand (50ns), I am going to
determin the most efficient interactions(the Hbond and non-bonded
interactions )  observed during 50 ns molecular dynamic simulations in
ssDNA-ligand complex. Using hbond command in gromacs I have see only 
the number of hydrogen bond,however I do not know what the second and
third columns represent in hbond.xvg?I used the following command for
Hbond analysis: HBOND –F trp_md.xtc –S trp_md.tpr –NUM trp_hnum.xvg 

Best regards 


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