[gmx-users] RDF

Tue Aug 29 04:58:30 CEST 2017

Thank you Sir

On Tue, 29 Aug 2017 at 6:33 AM, Dallas Warren <dallas.warren at monash.edu>
wrote:

> No idea what a surface distribution function is, and how it is
> generated.  But I suspect that those two are not the same.
> 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 23 August 2017 at 14:27, RAHUL SURESH <drrahulsuresh at gmail.com> wrote:
> > Thank you Sir,
> >
> > Is spatial distribution function is same as that of surface distribution
> > function?
> >
> > On Wed, Aug 23, 2017 at 9:39 AM, Dallas Warren <dallas.warren at monash.edu
> >
> > wrote:
> >
> >> https://www.google.com.au/search?q=gromacs+sdf
> >>
> >> i.e. gmx spatial
> >>
> >> Unfortunately, it only currently will work for a single reference
> >> molecule.  There use to be a g_sdf that would work for multiple copies
> >> of the reference, much in the same manner that gmx rdf does.  So if
> >> that is what you are after, you will need to install that older
> >> version and use that to generate it.
> >> 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 23 August 2017 at 13:27, RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
> >> > 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*
> >> >> >> > --
> >> >> >> > Gromacs Users mailing list
> >> >> >> >
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> >> >> >> >
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> >> >> >> >
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> >> or
> >> >> >> > send a mail to gmx-users-request at gromacs.org.
> >> >> >> >
> >> >> >> --
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> >> >> >>
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> > *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*
> > --
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*