Hi,
The ordering of masks is important in the RDF command. The literal meaning of:
> radial rdf_na_bin_50_2.dat 0.2 10 :2.P,OP?,O?P .Na+ volume center1
is "what is the probability I see residue 2 phosphate group atoms
(:2.P,OP?,O?P) as a function of distance from sodium atoms (.Na+)".
The center1 keyword means you're using the geometric center of the
phosphate group atoms, so instead of calculating 3x17 distances, its
just 17 (from center to each sodium atom). However, there is currently
a small bug in AT12 cpptraj 'center1' where 3x17 distances will be
used for normalization instead of just 17 (bugfix pending). You may
want to try something like:
radial rdf_na_bin_50_2.dat 0.2 10 .Na+ :2.OP?,O?P .Na+ volume
which is "what is the probability I see sodium atoms as a function of
distance from phosphate oxygens". In this case the normalization
should be done correctly.
-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 - 09:00:02 PST
