Hi Davide –


The solvation energy is dependent both on the size of the coarse grid and the resolution (grid spacing) of the fine grid.  I would recommend adjusting the resolution of the fine grid as well to see how this affects your results.



Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997



From: Davide Mercadante [mailto:dmer018@aucklanduni.ac.nz]
Sent: Friday, March 25, 2011 1:26 PM
To: apbs-users
Subject: [Apbs-users] Resolution of the coarse grid doesn't change the calculated energy in focusing calculations


Dear APBS users,


I have performed a series of focusing calculations (mg-manual) by setting a first coarse grid of dime 65 x 65 x 65 and various glen of 300^3, 250^3, 200^3 and 150^3.


The dimensions of the fine grid are the same and the glen are fixed in the three dimensions at 110. 


However, I have noticed that the calculated energy remains the same if I change the glen of the coarse grid leaving the glen of the fine grid fixed. 

I thought that being a focusing calculation the resolution of the coarse grid should affect the fine grid and therefore the energy calculated. 


I attach the file in the mail. Please note that the argument DIME for the keyword glen of the course grid has just be set for a script to recognize different values of glen for the coarse grid.


Can you please help me to understand why this happens and if I am wrong somewhere setting my calculations?


Any help will be highly appreciated.

Thank you. 





Davide Mercadante - PhD student -
Department of Chemistry
The University of Auckland
Rm 438 ext. 89171
1142 Auckland, New Zealand