Module: Molecule Electrostatics ()

Description:

This module calculates the electric or potential field around a molecule. Both potential and E-field can be evaluated both on a uniform grid or on a surface. The surface needs to be supplied as a data connection, while the grid will be computed in a spatial region which may be defined by a tab box.

To be able to compute the fields, the atom level of the molecule must contain a float attribute which contains the atomic partial charges. MMFF94 partial charges may be computed with the MoleculeEditor. Additionally a surface field may be supplied as a data connection, which contains surface polarization charges.

When choosing the voxel size, the resulting dimensions of the field will be shown. The user should keep in mind that the dimension does not only affect the memory usage but also the computation time, which might be excessively large if the molecule contains many charges. While the number of grid points of the field is dim.x*dim.y*dim.z, the number of function evaluations to compute the fields is the number of grid points multiplied by the number of charge centers different from 0.

The dielectric is assumed to be constant in space. To use inhomogeneous dielectrics you will need to use a program that solves the Poisson equation and import the generated field in .

Because of the inverse relationship with r, field values may become very large if grid points are close to charge centers. To avoid the implicated problems, the distance will be set to 0.01 Angstrom during the computation, whenever it is smaller than this minimum value.

Units of the calculated fields will be for the potential field and for the electric field, with being the unit of the charges supplied by the user in the charge attribute.

Ports:

Dielectrical Constant

Sets the dielectric constant.

Calculation Type

Allows the user to switch between the calculation of the electrostatic field which will create a vector field object or potential field which will generate a scalar field object.

Charge Attribute Name

The name of the float attribute that gives the atomic charges for the calculation.

Output Type

The field may either be generated on a lattice or on a surface. If surface computation is used the surface needs to be supplied as an input object.

Sampling Options

Lattice Box

Toggles the dragger box that allows one to resize the lattice. This port is only visible if the output type is 'lattice'.

Voxel Size

Allows you to adjust the voxel size of the lattice. This port is only visible if the output type is 'lattice'.

Dimensions

Shows the number of grid points in x, y, and z direction. This port is only visible if the output type is 'lattice'.