Re: [Apbs-users] Boundary Condition

[Nathan B. <ba...@bi...>]

Hi Sekwan --

The Dirichlet condition is applied at all sides of the box; however, it 
is not necessarily zero -- it is usually assigned based on an 
asymptotically-correct approximate solution to the PBE (see 
http://agave.wustl.edu/apbs/doc/html/user-guide/x594.html#bcfl).  Since 
this is just an approximation, you can definitely encounter problems if 
the box size is too small.  In particular, the box sizes for the various 
boundary conditions should vary as "bcfl zero" > "bcfl sdh" > "bcfl mdh" 
 > "bcfl focus".

The tool psize.py (see 
http://agave.wustl.edu/apbs/doc/html/user-guide/x371.html#AEN415) will 
help you determine the best box dimensions.

Thanks,

Nathan

Sekwan Oh wrote:

> Hi,
> 
> I have a question with the boundary condition.
> 
> Is it Dirichlet boundary condition on each side of the box? (zero 
> petential)
> 
> If not, are we having incorrect solution if we set the size of the box 
> smaller than it should be?
> 
> Can APBS estimate the reasonable size of the box so that Dirichlet BC 
> holds?
> 
> 
> Thank you.
> 
> Sekwan
> 
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-- 
Nathan A. Baker, Assistant Professor
Washington University in St. Louis School of Medicine
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
Phone:  (314) 362-2040, Fax:  (314) 362-0234
URL:  http://www.biochem.wustl.edu/~baker