The very last notice/inspiration:
Beside the actual possibilities :
RDF ( A -> B)
and
RDF ( center(A) -> B )
and the possibility which I was talking about:
RDF ( A -> center(B) )
there is of course the last one:
RDF ( center(A) -> center(B) )
this one might be interesting e.g. for some "coarse-graining" guys.
Best,
Marek
Dne Fri, 01 Feb 2013 21:40:07 +0100 Marek Maly <marek.maly.ujep.cz>
napsal/-a:
> Hi Thomas,
> thanks for your contribution but after that long discussion with Daniel
> I finally arrived to 2 very clear and simple questions. Which could
> explain all.
> Instead I got this comment from you which is rather some next step e.g.
> for the case
> that my interpretation of the #2 is wrong although is in well agreement
> with
> the relevant definition in AT12 manual and for the case that I am
> going to modify radial-cpptraj source. So please let's first answer that
> my last
> 2 questions. It seems that I should answer them by myself :))
>
> The main question was about the right interpretation of the command
>
> #2
> radial WAT_gCEN.RDF 0.2 30.0 :CEN :WAT noimage center1
>
> I just verified that this command is working according to the Daniel's
> interpretation e.g. that it is really calculating the RDF of the
> geometric
> center
> of the atoms in CEN residue/s with the respect to the WAT atoms.
>
> To verify this fact with my one-atom CEN residuum was very easy, because
> if Daniel is right the command #2 should provide in my special case
> identical result as command.
>
> #3
> radial WAT_gCEN.RDF 0.2 30.0 :CEN :WAT noimage
>
> e.g. #2 without center1 keyword. As I learned, #2=#3.
>
>
> The fact is, that such behavior is really not the one described in AT12
> manual
> (page 189) :
>
> AT12 CITATION IS:
> ***************************
> "If the center1 keyword is given, the RDF of all atoms in <mask2> to the
> geometric center of atoms in <mask1> is calculated."
> **************************
>
> I hope you both agree here :)) Would be a great idea to correct the
> source
> code
> (or the AT12 manual) so that the real behavior of the "radial" action is
> perfectly in agreement
> with what is written in the AT12 manual.
>
> Anyway I would vote here that instead or beside the possibility to
> calculate the RDF of the geometry center of some atoms to the another
> atoms (actual real possibility activated by "center1" keyword) there is
> in
> future added the possibility which I was talking about from the very
> start
> e.g.
> to calculate RDF of some atoms respect to the geometry center (or/and
> center of mass) of another
> group of atoms. In reality this would be very useful e.g. for the
> situations when one need
> to calcualte radial density profiles of different components respect to
> the center of some
> molecule/s under study, because not in every case it is so simple to find
> in such molecular structure some proper atom which during whole
> simulation
> (on all frames) sufficiently well
> can approximate/substitute geometric center or center of mass.
>
> Maybe that this feature is available in VMD (I am not sure right now) or
> in another SW but
> perhaps nobody will reproach you if it is implemented also in
> radial-cpptraj action :))
>
> Thanks for all comments and nice weekend to all !
>
>
> Best wishes,
>
> Marek
>
>
>
> Dne Fri, 01 Feb 2013 19:30:48 +0100 Thomas Cheatham <tec3.utah.edu>
> napsal/-a:
>
>>
>> You need to look at the equations for the radial distribution function.
>> The key is this "scaling factor" which is in fact the density. From the
>> old ptraj source:
>>
>> /*
>> * output Allen & Tildesley style histogram, i.e.
>> *
>> * histogram[bin]
>> * ----------------------------------------------------------
>> * (4/3)*pi*density*[(R+delR)**3 - R**3] * frames * molecules
>> */
>>
>> Depending on how you specify the density (it defaults to a particular
>> value), you will get the same result and the density choice differs
>> depending on your reference (the first mask).
>>
>> If you want the behavior to be as you suggest, you are going to need a
>> means to either use the system volume or re-write the code to do the
>> normalization in the way you think it should be done.
>>
>> -tec3
>>
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>
>
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Received on Fri Feb 01 2013 - 13:30:02 PST
