## [Apbs-users] Boundary Condition

 [Apbs-users] Boundary Condition From: Sekwan Oh - 2004-05-25 21:30:00 ```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 ```

 [Apbs-users] Boundary Condition From: Sekwan Oh - 2004-05-25 21:30:00 ```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 ```
 Re: [Apbs-users] Boundary Condition From: Nathan Baker - 2004-05-26 13:18:53 ```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 > > _______________________________________________ > apbs-users mailing list > apbs-users@... > http://cholla.wustl.edu/mailman/listinfo/apbs-users -- 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 ```