[Apbs-users] Calculating Potentials from Charge Density
Biomolecular electrostatics software
Brought to you by:
sobolevnrm
From: Bob J. <rob...@ph...> - 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 |