[gmx-users] RDF

[Dan Gil]

>
> I have come across people describing RDF analysis between water and water
> and I always wonder what does it means. RDF can be done between protein and
> water to know the distribution of water around protein with default center
> of mass(My little knowledge) and what co-ordination number contribute to
> RDF has always been a puzzle for me.
>

what do you mean by  two component system?
>

These questions be answered together at once. Imagine that a protein is
dissolved in water and urea solution. This system has 3 components (water,
urea, and protein). So there can be 6 RDFs: g_ww, g_uu, g_pp, g_wu, g_wp,
g_up. "w" means water, "u" means urea, "p" means protein (If there is only
one protein molecule, than g_pp should be zero).

Like you said, we can study the distribution of water around proteins. You
can also use RDFs far more things than just protein systems. It can be used
for salts in water, mixtures of organic solvents, etc.

Coordination number is related to the radial distribution function. This
Wikipedia page (https://en.wikipedia.org/wiki/Coordination_number) has a
one method of calculating the coordination number from RDFs. For example,
in a protein + water + urea system, you may be able to find the number of
water molecules and the number of urea molecules around the protein in each
solvation shell. These numbers are averages over time, not the actual
number at a moment in time. I think this method of calculating CN might be
a quick and easy way to see if its worth using better methods (e.g.
deconvoluting each solvation shell before integration). If your protein is
very large, I can imagine this being a more difficult problem, but I don't
know for sure.

On Fri, Aug 18, 2017 at 7:47 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
wrote:

> Hi Dan
>
> Thank you so much for you descriptive answers. I have few clarifications
> that I have posted here. I will go through the papers here.
>
> On Fri, Aug 18, 2017 at 5:01 PM, Dan Gil <dan.gil9973 at gmail.com> wrote:
>
> > Hi Rahul,
> >
> > I can't find the exact papers right now, but I remember seeing some
> > inconsistency in how people name these functions especially the radial
> > distribution function and pair correlation functions.
> >
> > If we go far back into literature, we can see JG Kirkwood using pair
> > correlation functions as functions of both the distance and the relative
> > orientation between the pairs [The Journal of Chemical Physics 19, 774
> > (1951); doi: 10.1063/1.1748352]. I don't know if he is the "inventor" of
> > the RDF, but he was one of the earliest to use it extensively in
> theories.
> > When you average the pair correlation functions over the relative
> > orientations, you get the radial distribution function which is a
> function
> > of distance only.
>
>
> That was very informative. But as now it can be calculated as a whole
> easily using various tools.
>
>
> > I think I've seen newer papers use RDF/PCF/PDF somewhat
> > interchangeably although I can't find these right now... Most people mean
> > the RDF but you can always look at the data to know what they mean.
> >
>
> I have come across people describing RDF analysis between water and water
> and I always wonder what does it means. RDF can be done between protein and
> water to know the distribution of water around protein with default center
> of mass(My little knowledge) and what co-ordination number contribute to
> RDF has always been a puzzle for me.
>
> >
> > I never used surface distribution functions, hopefully someone else can
> > bring you up to date on that one (How is the surface defined?).
> >
>
> I will be happy if some one can explain SDF and any particular tool to
> analyze it.
>
> >
> > But there is also the spatial distribution functions, which now a
> function
> > in 3D spherical coordinates. It gives the average density of particles at
> > given (r, theta, phi). In this paper they normalize it by the bulk
> density,
> > I am not sure if everyone does the same. (doi: 10.1063/1.465158)
> >
>
> Thank you. I guess it can be calculated using gmx spatial
>
> >
> > I think "radial pair distribution function" is synonymous with the RDF
> like
> > you said.
> >
>
> Yeah VMD use it as Radial pair distribution function.
>
> >
> > Partial radial distribution function is for multicomponent systems. In a
> > single component system, there is only one RDF and that is the total RDF.
> > In a two component system,
>
>
> what do you mean by  two component system?
>
>
> > there are 3 (AA, AB, BB) partial radial
> > distribution functions.
> >
> > Hope that helps!
> >
> > Dan
> >
> > On Fri, Aug 18, 2017 at 2:19 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
> > wrote:
> >
> > > Radial Distribution Function, Surface Distribution Function(SDF),
> Radial
> > > Pair Distribution Function and Partial Radial Distribution Function.
> > >
> > > What makes the difference in all the four?
> > >
> > > Have gone through lot pages and literature. Somehow one or the other
> > piece
> > > of explanation confuses me.
> > >
> > > Can I have a short explanation of all?
> > >
> > > RDF and R-pair DF one and the same?
> > >
> > > How do I calculate SDF and Partial-RDF if it is different from others?
> > >
> > > --
> > > *Regards,*
> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
> > > --
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>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
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