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

[Quyen Vu Van]

The second column is interactions which satisfy both angle and distance
cutoff of hydrogen bond. The third column is just interaction satisfy
distance cutoff

On Sun, Aug 26, 2018, 23:03 mmousivand93 <mmousivand93 at ut.ac.ir> wrote:

> 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
>
> Maryam
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