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## Re: [Apbs-users] Calculating Potentials from Charge Density

 Re: [Apbs-users] Calculating Potentials from Charge Density From: Nathan Baker - 2007-04-03 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 Poisson-Boltzmann) 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/ ```

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 [Apbs-users] Calculating Potentials from Charge Density From: Bob Johnson - 2007-04-02 16:38:18 ```Hello everyone, 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 Poisson-Boltzmann) 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. 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? Thanks, Bob Johnson ```
 Re: [Apbs-users] Calculating Potentials from Charge Density From: Nathan Baker - 2007-04-03 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 Poisson-Boltzmann) 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/ ```