Re: [Apbs-users] Resolution of the coarse grid doesn't change the calculated energy in focusing cal
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From: Baker, N. <Nat...@pn...> - 2011-03-25 23:41:24
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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:dm...@au...] 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 |