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

João Henriques joao.m.a.henriques at gmail.com
Wed Feb 21 09:51:49 CET 2018

```Justin already properly addressed the original post, so I'll just add a few

> I have the RDF between Calpha-Ow, and it is showing a slight hump/peak
around 0.47nm.

So you've managed to calculate it then as Justin suggested? FYI the RDF
minimum occurs at a larger distance for C atoms (~5 Å) than for O and N
atoms (3.3-3.5 Å), so the peak you see at 4.7 Å seems about right.

> 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...

Maybe I'm just not seeing the full picture, but how does this have anything
to do with the RDF? The RDF shows how density varies as a function of
distance from a reference particle. There certainly is some correlation
with particle orientation, but extracting this information from the RDF
profile alone seems unfeasible.

J

On Wed, Feb 21, 2018 at 5:00 AM, Dilip H N <cy16f01.dilip at nitk.edu.in>
wrote:

> 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
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==================================================
> >
> > --
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>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
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