No, it doesn't..without the center1 keyword, the value was going a bit
higher....i am attaching an image file in which RDF has been calculated
using the above command without the center1 keyword..
On Tue, Feb 5, 2013 at 11:38 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Out of curiosity, does the RDF look more like expected without the
> 'center1' keyword?
>
> -Dan
>
> On Tue, Feb 5, 2013 at 10:01 AM, Asmita Gupta <asmita4des.gmail.com>
> wrote:
> > I may be be missing some small point here : i want to calculate RDF of
> > Na+ ions around a nucleic acid backbone (which is a COUNT of the particle
> > as a function of distance) , i have used the following command :
> >
> > radial rdf_na_bin_50_2.dat 0.2 10 :2.P,OP?,O?P .Na+ volume center1
> > radial rdf_na_bin_50_3.dat 0.2 10 :3.P,OP?,O?P .Na+ volume center1
> > radial rdf_na_bin_50_4.dat 0.2 10 :4.P,OP?,O?P .Na+ volume center1
> >
> > Mask 1 has 3 atoms(in all cases); mask 2 i.e. total number of sodium ions
> > in my system is 17. Total system volume is : 205471.233980 Ang^3 . But
> on
> > the RDF plot, the value of y axis, is going till 25 which can't be
> possible
> > if the max ions is 17. I am confused about the normalization process?
> > Command used by me seems to be on a wrong track..surely..Can you please
> > suggest me a way as to how RDF of ions can be calculated using cpptraj
> >
> > Thanks
> >
> > Asmita
> >
> >
> > On Mon, Feb 4, 2013 at 10:07 PM, David A Case <case.biomaps.rutgers.edu
> >wrote:
> >
> >> On Mon, Feb 04, 2013, Asmita Gupta wrote:
> >> >
> >> > If i don't use the volume keyword, i have to mention some value
> using
> >> the
> >> > density keyword, as RDF has to be calculated for Na+; not for waters.
> How
> >> > to calculate this value...is it by using the regular
> >> (Density=mass/volume)
> >> > method??
> >>
> >> "density" in this context means number density, not mass density.
> >>
> >> ...dac
> >>
> >>
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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) 585-9119 (Fax)
>
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Received on Wed Feb 06 2013 - 01:00:03 PST
