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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--
-------------------------
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 Mon Feb 04 2013 - 08:00:04 PST
