[gmx-users] Calculate RDF within a certain distance from atom

[Dilip H N]

I have the RDF between Calpha-Ow, and it is showing a slight hump/peak
around 0.47nm. So, i am further interested in studying how water molecules
are oriented towards it closely...what is happening around within 0.7nm
distance of Calpha w.r.t Ow...

Any suggestions...??

Thank you.




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On Tue, Feb 20, 2018 at 10:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/20/18 11:53 AM, Dilip H N wrote:
>
>> Hello,
>> How to get RDF within a certain distance..??
>>
>> Say for eg., i have glycine amino-acid and i want the RDF of Oxygen water
>> atoms within 0.7nm of C-alpha (Calpha-Ow).
>>
>> how can i get it from in-house gmx rdf command...??
>>
>
> What do you hope to achieve from such a metric? RDF has to be normalized
> against bulk occupancy, which will of course not be achieved at a 0.7-nm
> distance. If you are interested in certain properties within given
> solvation shells, distances, etc. compute the normal RDF so that it is
> properly normalized and interpret the outcome of that calculation.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
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>
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student