Hello --

You are correct; the output should vary continuously. Can you please sent me the PQR and input file you're using so we can troubleshoot?

Thank you,

Nathan

 
From: Noriko Ozaki [mailto:nusausman@gmail.com]
Sent: Monday, April 08, 2013 04:02 PM
To: apbs-users@googlegroups.com <apbs-users@googlegroups.com>
Cc: Noriko Ozaki <nusausman@gmail.com>; APBS-USERS mailing list <apbs-users@lists.sourceforge.net>; Baker, Nathan
Subject: Re: [apbs-users] ndens and qdens
 
Thank you so much for clarifying the equations for ndens and qdens.

Based on this equation, mobile ion number density (ndens) is a function of the potential, which varies at each grid point.  So, the mobile ion number density should also change at each grid point.  However, the output I get is either 0.3000 or 0.0000 at all grid points (I set the negative and positive ion concentrations to be 0.150 and 0.150).  To me, this doesn't make sense.  Could you be able to explain to me why I am getting this result?  I am confused....

Thank you!!!


Noriko Ozaki

On Saturday, April 6, 2013 7:50:18 AM UTC-7, Baker, Nathan wrote:
Hello --

This is a good question; I apologize that our documentation wasn't clearer.  I've updated the official documentation at http://www.poissonboltzmann.org/apbs/user-guide/running-apbs/input-files/elec-input-file-section/elec-keywords/write with the equations used to calculate this output.

Thanks,

--
Nathan Baker
Pacific Northwest National Laboratory
Phone: +1-509-375-3997
http://nabaker.me

From: Noriko Ozaki <nusa...@gmail.com<mailto:nusausman@gmail.com>>
Date: Thursday, April 4, 2013 10:31 PM
To: APBS-USERS mailing list <apbs-...@googlegroups.com<mailto:apbs-...@googlegroups.com>>
Subject: [apbs-users] ndens and qdens

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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