Dear Daniel
>> It's not the number of waters that increases, but the number of potential
distances (maybe that is what you meant to say?).
Yes yes, the number of distances.
Thanks a lot again for all the suggestions and discussion.
best regards
Jiomm
On Wed, Apr 9, 2014 at 8:20 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Wed, Apr 9, 2014 at 11:15 AM, newamber list <newamberlist.gmail.com>
> wrote:
> > 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.
>
> It's not the number of waters that increases, but the number of
> potential distances (maybe that is what you meant to say?). The
> normalization factor will of course be related to the number of
> potential distances you can calculate, so if you have more potential
> distances there will be a correspondingly larger normalization factor.
>
> >>>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.
>
> The fact that you only have one chloride in your second mask is why I
> said you will have better statistics with your first mask. Of course
> if all you are interested in is that particular chloride then there is
> no issue.
>
> > 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?
>
> It will, but just for that particular chloride ion versus chloride
> ions in bulk. Also remember that cpptraj distance-based masks do not
> update on a frame-by-frame basis, so if you're using distance-based
> masks you have to make sure the ions are approximately where they
> should be over the course of the simulation (e.g. the one that starts
> out near your solute does not later move out into bulk).
>
> -Dan
>
> >
> > 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
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> >>
> >>
> >>
> >> --
> >> -------------------------
> >> 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)
> >>
> >> _______________________________________________
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> >>
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>
>
> --
> -------------------------
> 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)
>
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Received on Wed Apr 09 2014 - 14:00:03 PDT
