[gmx-users] RDF

Tue Aug 29 03:03:34 CEST 2017

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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>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > *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*
> --
> Gromacs Users mailing list
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