[gmx-users] g_hbond Issues

Mark Abraham Mark.Abraham at anu.edu.au
Sun Sep 13 18:11:58 CEST 2009

Anil Kumar wrote:
> Dear Gmx Users,
> I need to calculate the H-Bonds of simulation trajectory with specification
> of i to i+2/3/4/5 so on..and i to i -2/3/4/5 so on...separately.
> Do anyone have any idea how to do this...since the present option g_hbond
> calculate both the hydrogen bonds together irrespective of i to i+/-
> 2/3/4/5/6 and so on..
> Or is there any other program which can be used for this analysis.

Read g_hbond -h and/or consider creating suitable index groups with 
make_ndx in an index file to pass to g_hbond using -n.


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