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 Tue Feb 05 2013 - 10:30:03 PST
