8.4.1 Calculation of the Electrostatic Binding Energy

In this example, we illustrate how to calculate the electrostatic binding energy of a complex between two molecules. Assume that the molecules have segment identifiers of A and B.

     ! Calculate energy of the complex.
     pbe setup solvent 78.0 interior 2 all end -
         uniform boundary zero ionstr 0.15 -
         grid 0.4 temp 300.0 water 0.0 stern 2.0 -
         xdim 190 ydim 170 zdim 135 -
         all
     pbe potential maxiter 2000 rtol 1.0e-4
     pbe energy
     
     ! Calculate energy of segment A
     pbe setup solvent 78.0 interior 2 all end reuse -
         uniform boundary zero ionstr 0.15 -
         grid 0.4 temp 300.0 water 0.0 stern 2.0 -
         xdim 190 ydim 170 zdim 135 -
         clear atom A * *
     pbe potential maxiter 2000 rtol 1.0e-4
     pbe energy
     
     !Calculate energy of segment B
     pbe setup solvent 78.0 interior 2 all end reuse -
         uniform boundary zero ionstr 0.15 -
         grid 0.4 temp 300.0 water 0.0 stern 2.0 -
         xdim 190 ydim 170 zdim 135 -
         clear atom B * *
     pbe potential maxiter 2000 rtol 1.0e-4
     pbe energy

The electrostatic binding energy would be the difference between the first energy and the sum of the last two.

In this example, it should be noted that the calculations of each component are done using the same grid as the complex. This results in the clean subtraction of the self-energies.