Saturday, July 29, 2006

Electrostatic interactions software: DelPhi

DelPhi provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution. The current version is fast (the best relaxation parameter is estimated at run time), accurate (calculation of the electrostatic free energy is less dependent on the resolution of the lattice) and can handle extremely high lattice dimensions. It also includes flexible features for assigning different dielectric constants to different regions of space and treating systems containing mixed salt solutions.

DelPhi takes as input a coordinate file format of a molecule or equivalent data for geometrical objects and/or charge distributions and calculates the electrostatic potential in and around the system, using a finite difference solution to the Poisson-Boltzmann equation. DelPhi is a versatile electrostatics simulation program that can be used to investigate electrostatic fields in a variety of molecular systems.

New features of DelPhi include solutions to the nonlinear form of Poisson-Boltzmann equation which provide more accurate solutions for highly charged systems; solutions to mixtures of salts of different valence; solutions to different dielectric constants to different regions of space; higher precision in the finite difference scheme through the derivation of the expression for electrostatic free energy; and estimation of the best relaxation parameter at run time. All of these features enhances the speed and versatility of DelPhi to handle more complicated systems and finite difference lattices of extremely high dimension.

http:trantor.bioc.columbia.edu/delphi/


[+/-] show/hide this post  

0 Comments:

Post a Comment

<< Home