[Apbs-users] A question regarding energy and grid size

[Nathan A. Baker]

Dear Dr. Friedman --

It sounds like you are not calculating energies with the "self-energy"
terms removed.  These terms arise from the inclusion of the energies
of the non-delta-function charge distributions interacting with
themselves and are standard sources of grid artifacts (as you describe
below) in PB calculations.

If you want to know the electrostatic energy of a protein in solution
you should:
  1) Calculate the solvation energy from the difference of the
     energies of
     a) System with different sdie and pdie values
     b) System with both sdie and pdie set to the protein dielectric
  2) Add the Coulomb energy for the system of point charges in a
     medium with a dielectric constant of pdie.  You can use
     apbs/tools/manip/coulomb for this.
This procedure removes self-energies and is therefore much less
sensitive to grid spacings, positions, etc.

Thanks,

Nathan

Ran Friedman <ran@hemi.tau.ac.il> (10-19-2003 17:15:09+0200):
>Hi,
>
>I've tried to calculate the electrostatic properties of the same system
>(protein in water and salt) twice, using essentially the same settings
>except for the grid dimensions and number of points, as follows:
>
>run 1
>----
>
>  Grid dimensions: 161 x 161 x 161
>  Grid spacings: 0.400 x 0.400 x 0.400
>  Grid lengths: 64.000 x 64.000 x 64.000
>  Grid center: (9.745, 12.641, 21.402)
>
>run 2
>----
>
>  Grid dimensions: 193 x 193 x 193
>  Grid spacings: 0.333 x 0.333 x 0.333
>  Grid lengths: 64.000 x 64.000 x 64.000
>  Grid center: (9.745, 12.641, 21.402)
>
>The largest dimension of protein is 42 angstroms.
>
>Now as far as I understand it, I should expect that the results of run 1
>shouldn't be too different than the results of run2. However, what I got
>was:
>
>run 1
>----
>Total electrostatic energy = 1.551673825736E+05 kJ/mol
>
>run 2
>----
>Total electrostatic energy = 2.042898691098E+05 kJ/mol
>
>Am I missing something? Does the number of levels have an influence on
>the energy results? Or should I expect better convergence when the grid
>is smaller?
>
>Thank you,
>Ran.
>
>
>--
>------------------------------------------------------
>Ran Friedman
>Laser laboratory for fast reactions in biology
>Department of biochemistry
>Faculty of life sciences
>Tel-Aviv university
>972-3-6409824
>------------------------------------------------------
>
>
End of message from Ran Friedman.

-- 
Nathan A. Baker, Assistant Professor
Washington University in St. Louis School of Medicine
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
Phone:  (314) 362-2040, Fax:  (314) 362-0234
URL:  http://www.biochem.wustl.edu/~baker
PGP key:  http://cholla.wustl.edu/~baker/pubkey.asc