Next: , Previous: Energy Calculation Options, Up: Global Options for Conformational Search

12.4.5 Poisson-Boltzmann Options

By using the PBE option, it is possible to use electrostatic energies calculated using the Poisson-Boltzmann equation (PBE) in evaluating conformations. This code is still experimental, and is far from robust. In order to use it, you must first issue a PBE SETUP command, see PBE SETUP Command which constructs the grids using all the atoms that will be used in the conformational search. Also, using this code is very slow because solving the Poisson-Boltzmann equation is expensive. If you can use parallel processing to speed execution, you should use the LOOPS option in the PARALLEL command, see Parallel Command, in order to conserve memory.

Several possibilities for using the Poisson-Boltzmann equation are provided. By default, the Poisson-Boltzmann electrostatic energy substitutes for the Coulomb energy. If you specify the ONLY keyword, then the PBE energies substitute for the total energy. If you specify the SOLVATION keyword, then the electrostatic solvation energy is used. The electrostatic solvation energy is the difference between the Poisson-Boltzmann energy of the system with a solvent dielectric as specified in the PBE SETUP command and the Poisson-Boltzmann energy of the system with a solvent dielectric as specified in the VACUUM option. By default, the VACUUM dielectric is 1.0. The ONLY option can be specified with the SOLVATION option, and the result is that the electrostatic solvation energy substitutes for the total energy. The NEWB option specifies that the boundary be recalculated for each new conformation, whereas the FIXB option specifies the boundary be left untouched. NEWB is the default. An example of these options in use is given in Poisson-Boltzmann section, see PBE Examples.