Hi Nathan, thank you for your prompt response.

I still have a question: the "atomic radii of the biomolecule" means something like a "big atom" of radius of the dimensions of the biomolecule? I thought it should be something like many spheres of radius that of the atoms composing the biomolecule. If so, then it would probably better be defined as: "
The sphere radii are set to the atomic radii and the sphere charges are set to the atomic charges " without reference to the biomolecule.

Please, let me know if I am wrong

Marcel



En/na Baker, Nathan ha escrit:

Hello –

 

I apologize for the typo.  The correct statement should read

 

mdh

"Multiple Debye-Hückel" boundary condition. Dirichlet condition where the potential at the boundary is set to the values prescribed by a Debye-Hückel model for a multiple, non-interacting spheres with a point charges. The sphere radii are set to the atomic radii of the biomolecule and the sphere charges are set to the atomic charges of the biomolecule. This condition works better than sdh for closer boundaries but can be very slow for large biomolecules.

 

This has been fixed on the main webpage (http://is.gd/g8Bvt).

 

Thank you for bringing this to our attention.

 

__________________________________________________
Nathan Baker
Chief Scientist for Signature Science

Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, MSIN K7-28
Richland, WA  99352 USA
Tel:  509-375-3997
nathan.baker@pnl.gov  
www.pnl.gov

 

 

 

From: Marcel Aguilella [mailto:m_aguilella@hotmail.com]
Sent: Tuesday, October 19, 2010 6:49 AM
To: apbs-users@lists.sourceforge.net
Subject: [Apbs-users] bcfl flag

 

Dear apbs users,

In the apbs user guide I find the flags sdh and mdh for the bcfl keyword. The question is on the meaning of the second flag:

... Dirichlet condition where the potential at the boundary is set to the values prescribed by a Debye-Hückel model for a multiple, non-interacting spheres with a point charges. The sphere radii are set to the atomic radii of the biomolecule and the sphere charges are set to the total charge of the protein.

The problem I have comes especifically from the bold sentences above. Does that this mean several spheres with the atomic radii and charge of each atom, or a single sphere with the overall charge of the atoms (as in the sdh case)?

Can anyone clarify the above definition?

Thank you in advance

Marcel


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