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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Received on Fri Feb 01 2013 - 13:00:02 PST
