Hi Daniel
(I have changed email id as my mails were going to spam folder I think!)
Here is further disucssion and I have summarized things at bottom of mail.
>> The first is calculating the RDF from every water atom to all chloride
ions >>within 50 Ang. << of residues 484 and 441.
You mean how many waters are there in a shell of thickness dR around Cl-.
(a little correction actually am considering Cl ions which are greater than
50 Ang). which would represent a ion in bulk.
Actually my concern was that Avg. density increases when we use different
masks but actually the number of waters also increases as summed for all
shells (so numerator also increases! just not the denominator) as shown
below. Please correct me if wrong.
Lets take one bin only (say first shell of thickness dR) and just for a
single frame. So in a mask like this :WAT (:484,441>.50&:Cl-) I will have
such single bins around each Cl- (which are >50 Angs. far from COM of
484,441).
So RDF (for first shells) = sum of waters in all first shells around each
ion */* (#mask1*#mask 2 * Volume of shell)
which is rather equilvalent to average for all the ions if considered
individually= 1/M * (N1/#mask1* 1 * V + N2/#mask1* 1 * V .... Nn/#mask1* 1
* V) = (N1+N2.....Nn)/#mask1* #mask2* V
N1, N2.... Nn are number of waters in first shell of ions Cl1, Cl2... Cln
respectively
M = Total number of Cl ions (Cl1 to Cln) = #mask2
>> The second is calculating the RDF from every water to a single chloride
ion.
Again I think waters are there in a shell of thickness dR around Cl-.
>>They may be qualitatively similar, but you'll have better statistics with
the first one (and probably even better if you just make the second mask
':Cl-').
In second case it was just one ion actually I have many such single ions in
some region so will average for all ions and over all trajectory.
Summary: So in such case I think one can compare two plots quantitative as
well. Just considering the heights of peaks should tell me whether ions in
region of interest are more/less hydrated (second case) compared to ions in
bulk (first case). Please suggest if it does not make sense?
best regards
Jiomm
On Wed, Apr 9, 2014 at 3:22 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> You have a different average density because your second mask has a
> different number of atoms, so the number of things you expect in a
> volume slice will necessarily be different (you can see this by the
> vastly different number of 'distances' reported). Each plot is
> measuring different things. The first is calculating the RDF from
> every water atom to all chloride ions within 50 Ang. of residues 484
> and 441. The second is calculating the RDF from every water to a
> single chloride ion. They may be qualitatively similar, but you'll
> have better statistics with the first one (and probably even better if
> you just make the second mask ':Cl-').
>
> -Dan
>
> On Tue, Apr 8, 2014 at 8:12 PM, Jio M <jiomm.yahoo.com> wrote:
> > Hi All
> >
> > I have generated two RDF plots with different masks (for a single frame)
> and the output shows that both are using different avg. density for rdf
> calculation.
> > Please correct me if I am wrong how RDF is calculated here:
> >
> > RDF= density*[ Vol(R+dR) - Vol(R)]
> > Avg. density = (#mask1*#mask2)/avg. volume.
> >
> > I am just wondering in this case how we can compare both plots because
> avg. density used is different in both the cases? I have pasted here both
> commands with main outputs.
> >
> > 1) radial dat1 0.1 10 :WAT (:484,441>.50&:Cl-) volume
> >
> > ACTION OUTPUT:
> > RADIAL: 1 frames, 502721 distances.
> > # in mask1= 230148, # in mask2 = 1015, # in common = 0
> > Average volume is 2555636.055524 Ang^3.
> > Average density is 91.405902 distances / Ang^3.
> >
> >
> > 2) radial dat2 0.1 10 :WAT :514 volume # (514 is an Cl- ion)
> >
> > ACTION OUTPUT:
> > RADIAL: 1 frames, 396 distances.
> > # in mask1= 230148, # in mask2 = 1, # in common = 0
> > Average volume is 2555636.055524 Ang^3.
> > Average density is 0.090055 distances / Ang^3.
> >
> > thanks
> > Jiom
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 09 2014 - 10:30:03 PDT
