| DelPhi |
Boundary Command
The Setup/Boundary command defines the treatment of the grid points at the boundary of the DelPhi calculation grid. This includes the method used to assign values to the boundary points, as well as setting periodic bounds.
The Setup/Grid command defines and displays the 3-dimensional grid used in the DelPhi calculation. Three basic parameters must be specified to define the grid: the Grid Center, Grid Size, and Grid Resolution.
The Setup/Solute command defines the characteristics of the solute region, which consists of all points inside the solvent-accessible surface of the molecule.
The Setup/Solvent command defines the characteristics of the solvent region, which consists of all points outside the solvent-accessible surface of the molecule.
The Setup/Iterations command defines the form of the Poisson-Boltzmann equation used (linear or nonlinear), the number of iterations of each type, and the convergence criteria used to halt the calculation.
The Setup/Energies command specifies the electrostatic energy values which DelPhi calculates. DelPhi is capable of calculating the total electrostatic energy, the reaction field energy, and Coulombic energies of the molecule.
The Setup/Files command specifies the output files created by a DelPhi calculation, as well as the characteristics of the output data.
The Setup/Initialize command allows you to perform a calculation using some previously defined set of calculation parameters. The command reads a DelPhi parameter file (.prm) and sets all the associated Setup parameters.
The Setup/List_Setup command gives a brief list of the current DelPhi calculation parameter values.
The Run_DelPhi pulldown contains commands that are used to run a DelPhi calculation.
Run_DelPhi Pulldown
The Run_DelPhi/Host command is used to select the host computer on which the DelPhi job is run.
The Run_DelPhi/Run command creates the input files needed for the DelPhi calculation, and then runs the calculation as a background process or stores the command script for you to submit later. In addition, you may specify specific frames from an archive file as input coordinates, and an identical DelPhi calculation is performed on each frame.
The Potential pulldown contains commands that are used to compare and extract information from potential grids. These grids may be existing grid objects or they may be read from grid files.
Potential Pulldown
The Potential/Difference command allows you to add or subtract two potential grids, to obtain a third grid. The resulting grid can be used to determine regions where potentials are more or less positive in one grid than in the other.
The Potential/List command lists the potentials and electrostatic field values for a specified set of coordinates and total electrostatic energy. The list can be sent to the textport or to a file.
The Templates pulldown contains commands to create new, or modify existing, charge or radius template files. Such a file contains a series of templates (or rules) that specify the charge or radius value to assign to all atoms matching the template.
Templates Pulldown
The Templates/Charge_Edit command allows you to create or modify a charge template file. A charge template file can be specified using the Solute command of the Setup pulldown to assign atomic charges for a DelPhi calculation.
The Templates/Radius_Edit command allows you to create or modify a radius template file. A radius template file can be specified using the Solute command of the Setup pulldown to assign atomic radii for a DelPhi calculation.
The Grid pulldown is used to create and manipulate a potential grid for a given molecule. You may create and compute the potential grid, display and hide this grid, and write this grid to an output file that is readable by the Contour utility.
Grid Pulldown
The Grid/Get command retrieves grids from grid files.
The Grid/Put command allows you to write the grid data to a disk file. The output file name is specified in the File Name parameter. If no file extension is explicitly given, a default extension of .grd is added.
The Grid/Display command is used to control the display of grid objects. The Grid Attribute parameter controls which attribute of the grid to operate upon. The Point Set parameter specifies which points are set. The Alternate Space parameter specifies which axes to use.
The Grid/Color command is used to control the color of grid objects. The Grid Attribute parameter controls which attribute of the grid to operate upon. The Point Set parameter specifies which points are set.
The Grid/Histogram command plots a histogram of the scalar values of the grid points. The computation of histogram can be restricted to points with values which fall within a specified range. The coarseness of the histogram can be controlled by specifying the number of bins. The histogram can be plotted with linear or logarithmic scale heights.
The Grid/Contour command creates a set of contours from a specified Insight grid. One contour is created for each of the contour levels you specify. A contour level is a curve (or surface) connecting all of the points in the given grid which have the same value. These contours may be automatically displayed or left undisplayed.
The Contour pulldown contains commands that allow you to create and manipulate the display of contour objects and their labels. Contour objects are objects that display constant values throughout a set of grid data, such as are output by the DelPhi, DMol, or x-ray crystal refinement programs. Contours can be draw as dots, lines, or solid surfaces and represent equivalent values of a given quality of a molecule.
Contour Pulldown
The Contour/Create_Single command is used to create contours from grid files or grid objects. When reading from a grid file, a grid object is not created.
The Contour/Create_Range command is used to create contours from grid files or grid objects. When reading from a grid file, a grid object is not created.