[gmx-users] g_hbond

[Mark Abraham]

Dechang Li wrote:
> Dear all,
>    I have two moleculars in the .trr. I want to use g_hbond to analyze the 
> hydrogen bonds between them. Can g_hbond analyze the hydrogen bonds between
> two moleculars associated by a H2O molecular? The hydrogen bond may be the 
> following form:
>  
> 
>    
>      -N-H....O-H....O=C-
>              |
>              H   

Not natively. You could hack something together to find the frames where
 each of the -NH and OC- were forming a hydrogen bond, and then inspect
by hand to see if there was a bridge forming. Otherwise, you'd have to
hack the source code.

Mark