This section contains information on the parameters that can be altered during an electrostatics calculation run. The sample file is called prm. There are instructions on how to alter the parameters with the prm file.

The largest gridsize available with this version of Qnifft is 65x65x65. Smaller gridsizes can be used but larger ones cannot (default=65).

You must choose one of the following to determine how the molecule fits within the grid:

• scale: User manually inputs the dimensions for grids per angstrom (higher number gives greater resolution).

ex. sizing=scale scale=1.0

• fill: User determines what the longest dimension of the molecule as percentage of box length will be.

ex. sizing=fill fill=50

• border: User determines the closest distance (in angstroms) a molecule can be with respect to the boundary (default setting).

ex. sizing=border border_solvent=10

There are four choices for boundary conditions (I do not know what the "field" condition does). The condition must be inputted as boundary_condition=xxx

• zero: All boundary points have zero potential. This is a rather inaccurate method but requires minimal computing. Most useful if the molecule being analyzed is very small.

• dipolar: All boundary points have coulombic potentials as calculated from the center of positive charge and from the center of negative charge. This method is more accurate than "zero" and also requires minimal computing.

• coulombic: All boundary points have coulombic potentials as calculated from each point charge within the system studied. This is much more accurate than "zero" or "dipolar" but requires more computing (default setting).

• focussing: This requires two calculation runs. The first run should be done with one of the other conditions above, but at low resolution (i.e. at low grids per angstrom). The phi-map generated in the first run is then used as the basis for calculating the boundary potentials in the second "high-resolution" run.

• dielectric: Input the value for the dielectric of the interior of the molecule (default=2).

• spherical charge: Usually kept as false (default=f).

• dielectric: Input the value for the dielectric to the exterior of the molecule (default=80).

• salt concentration: Input the value (in molar) for the concentration of a 1:1 salt to be calculated within the solvent (default=0.145, which gives a Debye-Huckel radius of 8 angstroms).

• probe radius: Input the radius size of a sphere which will "roll" on the surface of the molecule. This determines the accessible van der Waals surface (Conolly method???) of the molecule (default=1.4).

• ionic radius: Input the radius of a sphere which will roll on the surface of the molecule. The distance from the center of this sphere to the van der Waals surface of the molecule determines an area of solvent that is inaccessible to ions in the solvent (i.e. dielectric=80, ionic strength=0) (default=2.0).

• temperature: Input the temperature (in Kelvin) for which the calculations shall be done (default=298).

• nonlinear equation: Determines if the nonlinear Poisson-Boltzmann equation is to be used in calculating electrostatics (default=t).

• convergence: Determines the value at which the iterations are considered to be converged (default=0.001).

• relaxation parameter: Kept as 1.0 (default=1.0).

• check frequency: Kept as 2 (default=2).

• newton iterations: Determines maximum number of iterations to be performed (default=20).

• level 0 multi-grid: Kept as 2 (default=2).
• level 1 multi-grid: Kept as 4 (default=4).
• level 2 multi-grid: Kept as 8 (default=8).
• level 3 multi-grid: Kept as 16 (default=16).

• smooth dielectric: Kept as 0 (default=0).

• concentration output: ? (default=f)

• Insight format: Determines if output pdb files will be in Insight format (default=f).

• site potentials: Determines if a file containing site files will be output (default=f).

• atom file output: Determines if a file containing atoms and their assigned partial charges will be output (default=f).

• analyse map: ? (default=f)

• title: ? (default=untitled)

• radius file: Specifies a file (click here for an example) that contains atomic radii.

• charge file: Specifies a file (click here for an example) that contains partial atomic charges.

• site charge file: ?

• PDB input file: Specifies a PDB file on which the electrostatic calculations will be performed.

• phi input file: Specifies a phi-map to be used in calculating boundary potentials. This is used in the focussing technique.

• site input file: Specifies a PDB file whose site potentials will be determined.

• PDB output file: Gives a name to a file to be written that contains the PDB file used as the partial charges assigned to atoms during the calculation.

• phi ouput file: Gives a name to a file to be written that contains the phi-map (Grasp readable) for the calculations performed.

• dielectric map file: Gives a name to a file that shows the dielectric map.

• site output file: Gives a name to a file to be written that contains electrostatic potentials at sites provided by the site input file.