Hello –


The Born ion electrostatic potential should vary inversely with the radius of the ion:  http://www.poissonboltzmann.org/apbs/examples/solvation-energies/solvation-energies-born-ion


The atompot function calculates the electrostatic potential from a particular calculation at the atom locations of the molecule.




Nathan Baker
Chief Scientist for Signature Science
Pacific Northwest National Laboratory


From: Vladimir Lankevich [mailto:vladimir.lankevich@gmail.com]
Sent: Thursday, July 22, 2010 1:05 PM
To: apbs-users@lists.sourceforge.net
Subject: [Apbs-users] how does electrostatic potential inside an atom works


Dear APBS-developers,

I have a question about pot and atompot functions of APBS. I need to know potential inside the atom and in its proximity, and at first I was just playing with Born atom to understand how everything works. I noticed that the potential inside the atom changes if I change the radius of this atom. Can you please explain why does this happen? How does APBS calculates the potential inside the atom? How does the atompot function calculates its output? I apologize if those are naive questions, but I could not find an answer in other places. Thank you.

Vladimir Lankevich