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.

 

Thanks,

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

http://signatures.pnl.gov

 

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. 

 

Cheers,

Davide

 


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