[gmx-users] RDF

[RAHUL SURESH]

Dear Warren,

Thanks a lot. How will I be able to calculate SDF using Gromacs..?



On Wed, 23 Aug 2017 at 8:19 AM, Dallas Warren <dallas.warren at monash.edu>
wrote:

> SDF (Spatial Distribution Function) is simply a three dimensional RDF.
> So instead of simply having a probability associated with each radius
> (r), it provides a probability associated with each (x,y,z) point.
>
> VMD can display the SDF generated by GROMACS.
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 18 August 2017 at 21:47, 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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> >> >
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> >
> >
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*