Hi Daniel
>> Bugfix 10 in particular fixed the normalization in the 'intrdf' plot
I am using latest bug fix AMBER and AMBERTOOLS, so that must include bugfix
10.
regards
Jiomm
On Wed, Apr 9, 2014 at 3:28 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi, what version of cpptraj are you using? Bugfix 10 in particular
> fixed the normalization in the 'intrdf' plot.
>
> -Dan
>
>
>
> On Mon, Apr 7, 2014 at 8:33 PM, Jio M <jiomm.yahoo.com> wrote:
> > Hi All
> >
> > I am using radial function to plot RDF of K ions around center of mass
> of O atoms. I have around 2100 K+ ions and octahedron box (149.1524703
> 149.1524703 149.1524703)
> >
> > radial temp.dat 0.1 95 :K+ :1-389.O volume intrdf temp_int.dat
> >
> >
> > I should get almost exact number of K+ in my box after integrating. I
> have following queries:
> >
> > 1) The integral values goes upto 1076448 which is too high. Also what
> should be max bin size in this case to get expected number of ions? I have
> chosen 95 because the RDF plot shows fall at 95 Angstroms (also it confuses
> me as box size dimension goes upto 149 Angstroms and I should see a fall
> around 140 or so)
> >
> > 2) Also I have one more query regarding 'volume' key word used here. In
> manual it says
> >
> > ".. if the volume keyword is specified the density is determined from
> the average volume of the system over all Frames."
> >
> > So in this case does this mean density is a 'number density' which is =
> (total number of K+ ions in a box / avg. volume of box)
> >
> > thanks
> > JIom
> > _______________________________________________
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> > 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)
>
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Received on Wed Apr 09 2014 - 10:30:04 PDT
