[gmx-users] g_hbond index

[Kavyashree M]

Ok thank you.

kavya

On Wed, Dec 19, 2012 at 10:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/19/12 11:43 AM, Kavyashree M wrote:
>
>> 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.
>>
>>
> You see a difference likely because you are invoking the command
> incorrectly (with overlapping index groups) and it is affecting the way the
> donor and acceptor arrays are constructed.  The proper method of analysis
> is to monitor H-bonds within "group 18" and then between "group 18" and
> whatever part of the protein that does not overlap with it.
>
>
> -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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