From beroza # - at - # scripps.edu Mon May 12 11:42:42 1997 Received: from relay1.scripps.edu for beroza[ AT ]scripps.edu by www.ccl.net (8.8.3/950822.1) id LAA20959; Mon, 12 May 1997 11:41:58 -0400 (EDT) Received: from euler.scripps.edu (euler.scripps.edu [137.131.252.34]) by relay1.scripps.edu (8.8.5/TSRI-1.5) with ESMTP id IAA16241; Mon, 12 May 1997 08:41:27 -0700 (PDT) Received: (from beroza |-at-| localhost) by euler.scripps.edu (8.8.5/TSRI-1.4) id IAA10348; Mon, 12 May 1997 08:40:59 -0700 (PDT) Date: Mon, 12 May 1997 08:40:59 -0700 (PDT) From: Paul Beroza Message-Id: <199705121540.IAA10348 ^%at%^ euler.scripps.edu> To: CHEMISTRY ":at:" www.ccl.net Subject: Numerically Solving Partial Differential Equations Cc: Gerald.Loeffler:~at~:univie.ac.at Gerald Loeffler wrote: > > The Delphi program by Barry Honig and co-workers solves the > Poisson-Boltzmann equation (a partial differential equation in > 3D-space) by using a FINITE DIFFERENCE method. > > I allways thought (without having considerable education in that field) > that such equations are best and quite easily solved by FINITE ELEMENT > methods. > > Hence I wonder if someone could recommend a good, famous, concise book > that deals with the general issue of how to numerically solve partial > differential equations so that I better understand the rational behind > Delphi's implementation. > Finite element methods will also work to solve the Poisson-Boltzmann equation. You (that's Tony You, not you personally) and Harvey (and probably others) did this a few years back. My understanding is that for large systems, like proteins, the number of elements required becomes quite large, and you can run out of memory. Finite element, finite difference, and boundary element methods can all be used to solve the Poisson-Boltzmann equation. I would recommend "Numerical Recipes" as a good introduction to numerical methods to solve partial differential equations. Paul --------------------------------------------------------------- Paul Beroza The Scripps Research Institute email: beroza(+ at +)scripps.edu Department of Molecular Biology phone: 619-784-9957 10550 N. Torrey Pines Rd. - TPC15 fax: 619-784-8896 La Jolla, CA 92037 URL: www.scripps.edu/~beroza ---------------------------------------------------------------