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Hello,
I am having trouble understanding and using qdens and ndens command.
I am interested in studying the difference in the mobile charge density
(qdens) and ion number density (ndens) between native and mutant proteins.
In the input file, I specified the concentrations of both negatively and
positively charged ions to be 0.150. The output .dx file from ndens
calculations shows either 0.300 or 0.000, and I am wondering if this is how
the result of ndens is supposed to be (0.150 + 0.150).
Also, what are the equations used to calculate ndens and qdens at each grid
point? The equation on the website
(http://www.ics.uci.edu/~dock/manuals/apbs/html/user-guide/x674.html) shows
that the ndens is a function of the potential. But, since the potential
changes at each grid point, then the ndens should give varying values at
each grid point as well. I am a little confused with what is going on with
ndens and qdens.
Any help will be truly appreciated. Thank you for your time.
Noriko Uka Ozaki
Ph.D. student
Department of Bioengineering
University of California, Riverside
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Hello,

I am having trouble understanding =
and using qdens and ndens command.

I am int=
erested in studying the difference in the mobile charge density (qdens) and=
ion number density (ndens) between native and mutant proteins. In th=
e input file, I specified the concentrations of both negatively and positiv=
ely charged ions to be 0.150. The output .dx file from ndens calculat=
ions shows either 0.300 or 0.000, and I am wondering if this is how the res=
ult of ndens is supposed to be (0.150 + 0.150).

=
Also, what are the equations used to calculate ndens and qdens at each=
grid point? The equation on the website (http://www.ics.uci.edu/~dock/manu=
als/apbs/html/user-guide/x674.html) shows that the ndens is a function of t=
he potential. But, since the potential changes at each grid point, th=
en the ndens should give varying values at each grid point as well. I=
am a little confused with what is going on with ndens and qdens.

Any help will be truly appreciated. Thank you for you=
r time.

Noriko Uka O=
zaki

Ph.D. student

Department of Bioengineering

University of California, Riverside
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