[Apbs-users] Total Polarization Charge

[Lifeng T. <lt...@us...>]

Hi Nathan

I am working on  a comparison study of Boundary element method (BEM) 
and APBS.

In our polarization charge approach, the computed polarization charge
can be compared with the analytical one to monitor the convergence of 
the calculation.

For example, a molecule of +1 proton charge will have an induced 
polarization charge of
-0.98726 based on the formula (Dout-Din)/(Dout*Din), where Din=78.5 and 
Dout=1.0.
If my calculation using the BEM gives a polarization charge of -1.20, I 
know there may be
large errors in the solvation energy and force.

Can APBS compute the overall polarization charge? What would you 
suggest to look for in
the APBS output file to check the results of the calculation?

Thanks!

Lifeng Tian
Depart of Chemistry & Biochemistry
Univ of the Sciences in Philadelphia
600 S 43rd street
Philadelphia, PA 19104