[gmx-users] g_hbond Issues

Anil Kumar chemanil at gmail.com
Mon Sep 14 04:27:16 CEST 2009

Dear Mark,

Thanks for your suggestions of including/using index file. This is fine but
is it not a cumbersome process to define for different length of systems in
this way! Since, one has to define/make the group for each carbonyl group
with other pairs!

Anyway for the time being I am using this strategy. But if anyway has other
options then kindly let me know.

Thanks in advance,
with warm regards,
IIT Bombay

On Sun, Sep 13, 2009 at 9:41 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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.
> Mark
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