[gmx-users] g_hbond index

[Kavyashree M]

Sir,

I thought that the order should not matter but when I used 18 - 1
and 1 - 18 the graph were slightly off.

Group 18 is a set of residues in that protein with some unique property.
I wanted to see the variation of Hbond of these residues with the whole
protein. so group 18 is a subset of group 1.


Thank you
Kavya
On Wed, Dec 19, 2012 at 10:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/19/12 9:37 AM, Kavyashree M wrote:
>
>> Dear users,
>>
>> While using g_hbond, does it make any difference if I give option
>> 18 and 1 or 1 and 18?
>>
>
> Order does not matter.
>
>
>  I wanted to find the hydrogen bonding of a group of residues with
>> the whole protein so I had an index of this group. When I give the
>> option as 18 (index number) and 1 (whole protein), I get several
>> messages
>> "Hm. This isn't the first time I found this donor (...,...)"
>> But later it does calculates. does this mean that it is double counting
>> those interactions?
>>
>>
> What is group 18?  Be mindful of the g_hbond requirement that the chosen
> groups must be completely unique or completely overlapping.
>
> -Justin
>
> --
> ==============================**==========
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> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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