From: Nathan Baker <baker@cc...>  20070403 15:38:07

Hi Bob  > I am trying to compute the electrostatic potential at the surface > of a carbon > nanotube in the presence of adsorbed DNA and water. Because I want > to treat the > water and counterions explicitly in my calculation, I'm interested > in solving > the Poisson (not PoissonBoltzmann) equation. First I would like to > calculate > the charge density (obtained from an MD trajectory) about the > nanotube and then > simply integrate it to obtain the potential at the nanotube > surface. This is > much less time consuming than trying to calculate the potential for > each frame > of the trajectory and time averaging the result. By integrating, do you mean simply integrating with the analytic Green function for that particular geometry and boundary conditions? Are you thinking of a infinite cylinder? If so, it seems like this might be most easily accomplished in Mathematica, Matlab, Octave, etc. > However, because of my particular geometry the charge density I > want to > calculate will be a function of x,y coordinates. It doesn't seem > like APBS can > compute the potential given the charge density. Does anyone know of > any > software that can? Does anyone have any other suggestions on how to > use APBS > for this calculation? You could do this in APBS for finite geometries. However, if you're integrating with a known Green function, then I think something simpler in Matlab or Octave would probably be a better option. Thanks, Nathan  Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ 