Hello --

This problem is due to an ambiguity in the user manual that has been corrected.  Previously, the "usemap diel" command was documented (http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#usemap) as
Dielectric function map (as read by read diel); this causes the pdie, sdie, srad, swin, and srfm parameters and the radii of the biomolecular atoms to be ignored when computing dielectric values for the Poisson-Boltzmann equation.

This statement has been clarified to read
Dielectric function map (as read by read diel); this causes the pdie, sdie, srad, swin, and srfm parameters and the radii of the biomolecular atoms to be ignored when computing dielectric maps for the Poisson-Boltzmann equation. Note that the pdie and sdie values are still used for some boundary condition calculations as specified by bcfl.

We have confirmed that the problem you describe is due to the effect of the "sdie" parameter on the boundary conditions.  In other words, the code is behaving as expected but the documentation was confusing.

Thank you for reporting this issue,

Nathan

2009/12/16 <przemekbartha@gmail.com>
Hello,
I am doing same research on solvation energy of an elipsoid that has got a dielectric constant equal 1, where surrounding area's constant is 80.
To do that, I implement my own "dx" maps. I have adapded one of examples to my needs.
My quastion is: where does the difference between calculation #1 (solvated state) and calculation #2 (reference state) come from, since I use the same maps in both calculations?
The difference is about 57kJ/mol. The energies are respectively ~2323kJ/mol and 2380kJ/mol.
Below, I attach my files.
 
best regards,
Przemek
 
 
APBS input file:
read
 mol pqr ion.pqr 
 diel dx 1.5_1.5_xelips_65.dx 1.5_1.5_yelips_65.dx 1.5_1.5_zelips_65.dx
 # diel dx mapax.dx mapay.dx mapaz.dx
end
 
elec name solv             # Electrostatics calculation on the solvated state
 
 
  mg-manual              # Specify the mode for APBS to run
  usemap diel 1
  dime 65 65 65        # The grid dimensions
  nlev 4                 # Multigrid level parameter
  grid 0.33 0.33 0.33    # Grid spacing
  gcent mol 1            # Center the grid on molecule 1
  mol 1                  # Perform the calculation on molecule 1
  lpbe                   # Solve the linearized Poisson-Boltzmann
                         # equation
  bcfl mdh               # Use all multipole moments when calculating the
                         # potential
  pdie 1.0               # Solute dielectric
  sdie 80                # Solvent dielectric
  chgm spl2              # Spline-based discretization of the delta
                         # functions
  srfm mol               # Molecular surface definition
 
  srad 1.4               # Solvent probe radius (for molecular surface)
  swin 0.3               # Solvent surface spline window (not used here)
  sdens 10.0             # Sphere density of accessibility object
  temp 298.15            # Temperature
  gamma 0.105            # Apolar energy surface coefficient (not used here)
  calcenergy total       # Calculate energies
  calcforce no           # Do not calculate forces
  write pot dx potential-RADIUS
                         # Write out the potential
 # write dielx dx mapax
 # write diely dx mapay
 # write dielz dx mapaz
 
end
 
elec name ref              # Calculate potential for reference (vacuum) state
 
 
  mg-manual
  usemap diel 1
  dime 65 65 65
  nlev 1
  grid 0.33 0.33 0.33
  gcent mol 1
  mol 1
  lpbe
  bcfl mdh
  pdie 1.0               # The solvent and solute dielectric constants are
                         # equal
  sdie 1.0               # The solvent and solute dielectric constants are
                         # equal
  chgm spl2
  srfm mol
  srad 1.4
  swin 0.3
  sdens 10.0
  temp 298.15
  gamma 0.105
  calcenergy total
  calcforce no
 
#  write diely dx mapay
#  write dielz dx mapaz
#  write kappa dx kappa
 
end
 
print
 
  energy solv - ref
 
end
 
quit
 
ion.pqr
ATOM      1  I   ION     1       4.000   4.000  4.000  1.00 1.5
 
 

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--
Nathan Baker (http://bakergroup.wustl.edu)
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Director, Computational and Molecular Biophysics Graduate Program
Center for Computational Biology, Washington University in St. Louis