Hi,
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??
In that case, Mass of Na+ is 22.9 and average volume of system is
168452.13 Ang^3.. ...so is the resultant value of density to be used in the
density keyword??
Thanks
Asmita
On Mon, Feb 4, 2013 at 9:06 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> The next line of output from cpptraj (after 'Average volume...') is
> something like:
>
> Average density is X distances / Ang^3.
>
> Cpptraj determines the number of distances calculated each frame
> (#atoms_mask1 * #atoms_mask2 - #atoms_in_common) and divides that by
> the average volume over all frames (calculated from box sizes) to
> arrive at the density.
>
> -Dan
>
>
> On Mon, Feb 4, 2013 at 3:08 AM, Asmita Gupta <asmita4des.gmail.com> wrote:
> > Dear users,
> >
> > To calculate RDF of Na ions from phosphate groups of nucleic acids, how
> > is density calculated if volume keyword is given..
> >
> > For example, i am using this command for RDF in cpptraj:
> >
> > radial rdf_na_bin_20.dat 0.5 10 .Na+ .P,OP?,O?P volume
> >
> > Average volume of the system is : 168452.135 (Ang^3)
> >
> > Thanks
> >
> > Asmita
> > _______________________________________________
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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) 585-9119 (Fax)
>
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>
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Received on Mon Feb 04 2013 - 08:30:03 PST
