## apbs-users

 [Apbs-users] Reading arbitrary dielectric maps into APBS From: Marcel Aguilella Arzo - 2008-06-26 14:59:35 ```Dear all, I'm interested in loading externally generated dielectric maps inside APBS. My question is: Should I read an arbitrary dielectric map into APBS (f.e. a linearly varying dielectric map between two sides of the computation box), will the computed potential map be the physical potential corresponding to such distribution? Mathematically, is the returned potential the solution to: div( eps(x)*div(V) )=-rho/eps0 ??? Or maybe APBS could not handle such problems correctly? My guess is that it should be, because the standard two region approach is just a special case of this more general problem, but I wanted to be sure. Best regards -- Dr. Marcel Aguilella-Arzo Dept. Física Universitat Jaume I 12071 Castellon SPAIN Email: arzo@... Phone: +34-964-728046 Fax: +34-964-729218 ```
 Re: [Apbs-users] Reading arbitrary dielectric maps into APBS From: Nathan Baker - 2008-06-26 21:30:52 ```Hello -- > I'm interested in loading externally generated dielectric maps inside > APBS. My question is: Should I read an arbitrary dielectric map into > APBS (f.e. a linearly varying dielectric map between two sides of the > computation box), will the computed potential map be the physical > potential corresponding to such distribution? The computed potential will obey Poisson's equation subject to the boundary conditions, dielectric map, and charge distribution you assign. > Mathematically, is the returned potential the solution to: > > div( eps(x)*div(V) )=-rho/eps0 ??? No, it's the solution to div( eps(x)*grad(V) ) = -rho/eps0 where V is the potential, rho is the charge distribution, etc.... > Or maybe APBS could not handle such problems correctly? Umm... why would you say that? > My guess is that it should be, because the standard two region > approach > is just a special case of this more general problem, but I wanted to > be > sure. Yes, APBS can handle a variety of dielectric definitions from discontinuous with two (or more) distinct dielectric regions to continuous, etc. Thanks, Nathan > > Best regards > > -- > Dr. Marcel Aguilella-Arzo > Dept. Física > Universitat Jaume I > 12071 Castellon > SPAIN > Email: arzo@... > Phone: +34-964-728046 > Fax: +34-964-729218 > > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://sourceforge.net/services/buy/index.php > _______________________________________________ > apbs-users mailing list > apbs-users@... > https://lists.sourceforge.net/lists/listinfo/apbs-users -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ ```