From: Nathan Baker <nathanabaker@ma...>  20061118 02:03:24

Hi Vyom  > So does it mean that the boundary grid points have their potentials > fixed not by the absolute position of the charges but by the > positions of these charges after they are distributed on the > neighboring grid points?? No, the boundary point potentials are determined by the exact charge locations, not the interpolated charges. The idea is that since the boundaries need to be far away from charges anyway, there's no need to distinguish between exact and interpolated delta functions. > As an example if a charge is at, say x=10.2 and I have grid points > at 10.0 and 11.0 then I distribute this charge at 10.0 and 11.0 and > use these distributed charge values to calculate the boundary > potentials in the case of poisson solver (and ofcourse this is the > same grid which I use to calculate the grid boundary potential > values for solving the PBE as well and not the actual position of > the charge). That's not the way it's currently implemented in APBS but this could be changed. However, I'm not sure what you'd want to do this... > I am thinking of only fluctuation in salt concentration which could > be thought of as a fluctuation in salt charges as well. However the > charge distribution on the molecule remains fixed throughout. APBS uses only a mean field grand canonical version of the PB equation  no salt fluctuations. Thanks, Nathan > On Nov 16, 2006, at 7:33 AM, Nathan Baker wrote: > >> Hi Vyom  >> >>> I have a few questions about how one gets rid of the self energy >>> contribution from the electrostatic energy. From what I understand >>> this >>> is done by doing two calculations, the first for the system whose >>> potential we want to determine(I will call it the test system) and >>> second using the same system but this time suspended in a medium of >>> same dielectric constant(which I call the reference system). One >>> then >>> subtracts the reference electrostatic energy from the test system >>> electrostatic energy to get the electrostatic energy of the test >>> system >>> less the self energy contribution. >> >> That's correct. >> >>> 1. Is it assumed that the Kappa (or free ion concentration) for the >>> reference medium is 0? >> >> Right. >> >>> And if so then this in principle means one is >>> solving the 3D poisson equation? >> >> Yes, but the discrete nature of the solution is important since we're >> interested in solving the 3D poisson equation for the same finite >> discretization charge distribution (e.g., approximations of delta >> functions) used in the test system to consistently eliminate self >> interaction energies. >> >>> 2. On assuming periodic boundary conditions (where one doesn't >>> specify >>> the potential value anywhere) does the difference in energies >>> turn out >>> to be the same as in the case of Dirichlet boundary condition? >> >> Not necessarily. If the periodic system is large enough, this >> approximation could work  but it would definitely need to be >> tested. >> >>> 3. For interactions among different molecules in the same system, >>> one >>> would have to add the dispersion energy terms to the electrostatic >>> energy as well (here I assume this includes only the VDW term and >>> not >>> the cavity term). In this case do the DLVO characteristics evolve >>> as a >>> function of salt concentration? [By DLVO characteristics I mean the >>> eventual agglomeration of molecules on increasing salt concentration >>> and the evolution of a secondary minima] >> >> I would guess the presence or absence of salt dependence would depend >> on what sorts of dispersion interactions you're thinking of >> (fluctuations in solution salt charges vs. fluctuations in charge >> distributions on the molecules vs. ...). Can you clarify? >> >> Thanks, >> >> Nathan >> >>  >> Assistant Professor, Dept. of Biochemistry and Molecular Biophysics >> Center for Computational Biology, Washington University in St. Louis >> Web: http://cholla.wustl.edu/ >> >> >> >>  >>  >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to >> share your >> opinions on IT & business topics through brief surveys  and earn >> cash >> http://www.techsay.com/default.php? >> page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> 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/ 