From: <przemekbartha@gm...>  20091216 16:15:28

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 mgmanual # 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 PoissonBoltzmann # equation bcfl mdh # Use all multipole moments when calculating the # potential pdie 1.0 # Solute dielectric sdie 80 # Solvent dielectric chgm spl2 # Splinebased 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 potentialRADIUS # 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 mgmanual 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 