[gmx-users] question about g_hbond

[Nidhi Katyal]

The two groups are:  protein and cosolvent molecules. With g_mindist -on ,
I am getting values of around 6500 per timeframe. But then why g_hbond
giving different results.


On Sun, Sep 1, 2013 at 10:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/1/13 12:50 PM, Nidhi Katyal wrote:
>
>> Hello,
>> I would like to calculate number of contacts between two groups, for which
>> I am using following command:
>> g_hbond -f *.xtc -s *.tpr -num *.xvg -contact -b 49000 -e 50000
>> I am getting 0 as the output. But when I am calculating number of hydrogen
>> bonds between the same two groups by using the above command without
>> contact option I  am getting 5.2 as the output.
>> My question is wouldn't number of contacts be higher than number of
>> hydrogen bonds since hydrogen bonds are subset of contacts.
>>
>
> In theory, but something might be failing.  What are the groups you are
> choosing?  What is your expected outcome?  What does the output of
> g_mindist -on give you?
>
> -Justin
>
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