From: Nathan Baker <nathanabaker@ma...>  20061115 11:43:58

Hi Magdalena  Vincent pointed you to the correct portion of the code for the =20 solver; the various charge distributions and problem coefficients are =20= specified in the Vpmg_fillco routines of vpmg.c. The details of the =20 solver methodology are also described in more detail in the following =20= references: Holst M, Saied F. Multigrid solution of the PoissonBoltzmann =20 equation. Journal of Computational Chemistry. 14 (1), 10513, 1993. Holst M, Kozack RE, Saied F, Subramaniam S. Protein electrostatics: =20 Rapid multigridbased newton algorithm for solution of the full =20 nonlinear PoissonBoltzmann equation. J Biomol Struct Dyn. 11 (6), =20 143745, 1994. Holst M, Kozack RE, Saied F, Subramaniam S. Treatment of =20 electrostatic effects in proteins: Multigridbased newton iterative =20 method for solution of the full nonlinear PoissonBoltzmann =20 equation. Proteins. 18 (3), 23145, 1994. Holst MJ, Saied F. Numerical solution of the nonlinear Poisson=20 Boltzmann equation: Developing more robust and efficient methods. =20 Journal of Computational Chemistry. 16 (3), 33764, 1995. and in an excellent summary based on Mike Holst's thesis: http://=20 cam.ucsd.edu/~mholst/pubs/dist/Hols94d.pdf Thanks, Nathan On Nov 14, 2006, at 11:58 AM, vincentc@... wrote: > > Magdalena  > > The file I think you're looking for is in the 'mypde.f' routine in =20 > the MG subdirectory of the APBS source: > > apbs0.4.0/src/mg/mypde.f > > In particular, the line(s) in the code of relevance are: > > line 384 in subroutine c_vec and line 517 in dc_vec where the non=20 > linear term its derivative are defined ... > > cheers, > > vince > > > > On Tue, 14 Nov 2006, magdalena gruziel wrote: > >> hello, >> >> i have a question concerninng the solution of the PB equation itself, >> or more precisly the definition of the problem to be solved. >> i understand, that pmg encompasses the (Fortran in general) =20 >> routines that >> solve the general eliptic differential equation. so the nonlinearity >> (the function c(u) given in these Fortran routines) has to be =20 >> defined before enetering >> given routine. >> where then, it happens? which procedure initiates the solver >> with the nonlinearity? in case of PB this is actually the form >> of mobile charge distribution. but where (in the source) to we =20 >> actually tell the solver how this distribution looks like? >> >> with kind regards >> magdalena >> >> >>  >> Champions On Ice  Olimpijscy mistrzowie ta=C5=84ca na lodzie! >> Zobacz spektakularne widowisko  Kliknij: >> http://klik.wp.pl/?adr=3Dhttp%3A%2F%2Fadv.reklama.wp.pl%2Fas%=20 >> 2Fd33.html&sid=3D927 >> >> >> >> =20= >>  >> Using Tomcat but need to do more? Need to support web services, =20 >> security? >> Get stuff done quickly with preintegrated technology to make your =20= >> job easier >> Download IBM WebSphere Application Server v.1.0.1 based on Apache =20 >> Geronimo >> http://sel.asus.falkag.net/sel?=20 >> cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D121642 >> _______________________________________________ >> apbsusers mailing list >> apbsusers@... >> https://lists.sourceforge.net/lists/listinfo/apbsusers > =20= >  > SF.net email is sponsored by: A Better Job is Waiting for You  =20 > Find it Now. > Check out Slashdot's new job board. Browse through tons of =20 > technical jobs > posted by companies looking to hire people just like you. > http://jobs.slashdot.org/=20 > _______________________________________________ > apbsusers mailing list > apbsusers@... > https://lists.sourceforge.net/lists/listinfo/apbsusers  Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ 