Inorganic Builder Plugin, Version 0.1

The inorganicbuilder plugin provides tools for many of the functions needed to set up simulations of molecules and inorganic structures. The functions of the plugin are organized into several Tasks. These tasks are selected from the Task menu.

Build device

This task lets you set up the basic parameters, including material and dimensions, for the initial device structure. The following values describe the structure:

• Material: Select a material to specify the corresponding unit cell and basis cell dimensions. Additional materials can be added to this menu using the text interface.
• Hex box: For materials with hexagonal symmetry in the X-Y plane, checking this box will convert the structure to a hexagonal form.
• Origin: Specify the coordinates of the center of the device
• Box dimension: Three integers specify the number of unit cells in the A, B, and C directions. When using hexagonal symmetry, Diameter defines the diameter of the inscribed cylinder, and height defines the number of unit cells in the Z dimension.
• Output file: The file name to store the resulting PSF/PDB files

Clicking Draw Box after specifiying the box parameters will construct a wire frame outline of the device (including any exclusions) in the VMD OpenGL window.

In addition, you may cut regions out of the unit cell before you construct it, by Adding exclusions, regions to remove from the structure before constructing the PSF/PDB files. Defined regions can be removed before construction by selecting one and clicking Remove exclusion.

Several different types of exclusions are available for constructing the device:

• Parallelopiped: Specify one corner of the parallelopiped, and the three vectors defining the three edges intersecting at that corner.
• Cylinder: Specify the centers of the bottom and the top of the cylinder, as well as the radius.
• Sphere: Specify the center and radius of the sphere.
• Cone: Specify the center of the base of the cone, the apex, and the radius of the base.
• Tetrahedron: Specify one corner of the tetrahedron, and the three vectors defining the three edges intersecting at that corner.
• VMD selection: Specify a VMD selection (using the syntax of the atomselect command) to either include or exclude. Selections will be applied in the order that they are added to the exclusion list. VMD selection exclusions will not show up when the Draw Box button is used, since they must be applied while the structure is being filled with atoms.

After defining the device size and all desired exclusions, press the Build structure button to construct the model. Clicking Cancel closes the plugin window.

Add periodic bonds

When reading in a structure with no bond information, VMD uses a distance-based algorithm to guess the bonds. This algorithm works well for many models, but does not take into account bonds that wrap around the walls of a periodic cell. This task enhances the built-in VMD bond search algorithm by also adding the bonds that wrap around the periodic cell. The following parameters are available:

• Molecule: Select a structure, either by selecting a molecule already loaded in VMD, or by selecting the PSF and PDB files for a stored structure.
• Origin and Basis: If you just created this structure, the Origin and Basis parameters will be carried over from the Build Crystal task, otherwise, enter the Origin (center of the box) and the basis vectors for the periodic box.
• Bond cutoff: Select a bond cutoff radius (in angstroms) appropriate for the material in use.
• Transform to hex on completion: If the basis vectors of the device allow it to be represented with hexagonal periodicity, the structure will be stored in that form.
• Build angles/dihedrals: After building the two-atom bonds, also generate angle and dihedral bonds
• Load result: After generating and storing the structure, load it in to VMD
• Output file: The name of the PSF/PDB files of the structure with bonds

After defining these parameters, press the Build Periodic Bonds button to construct the model. Clicking Cancel closes the plugin window.

Add specified bonds

For some materials, the VMD distance-based bond search does not generate correct bonds. For instance, with amorphous silicon dioxide, VMD's distance-based search yields many incorrect O-O and Si-Si bonds in addition to the desired Si-O bonds. This task lets you specify which types of atoms may be bonded, and the maximum length of each bond type. The following parameters are available:

• Molecule: Select a structure, either by selecting a molecule already loaded in VMD, or by selecting the PSF and PDB files for a stored structure.
• Origin and Basis: If you just created this structure, the Origin and Basis parameters will be carried over from the Build Crystal task, otherwise, enter the Origin (center of the box) and the basis vectors for the periodic box.
• Build angles/dihedrals: After building the two-atom bonds, also generate angle and dihedral bonds
• Output file: The name of the PSF/PDB files of the structure with bonds
• Load result: After generating and storing the structure, load it in to VMD

Specify what element types should be bonded by pressing the Add bond button. Enter the two element names and the maximum radius for the bond. The Remove button can be used to get rid of unwanted bond types.

After defining these parameters, press the Find Bonds button to construct the model. Clicking Cancel closes the plugin window.

Find surface/interior atoms

This task allows a device to be separated into two sets of files, one containing atoms within a certain distance of the surface, and the other containing the interior atoms. The shell of surface atoms is defined by its proximity to vacuum. A grid is placed over the volume of the periodic cell, and each grid point is considered a vacuum grid point if no atoms fall within a sphere (bubble) of radius r centered on that grid point. Then, surface atom shell of the desired thickness t is determined by selecting all atoms closer than r + t of a vacuum grid point. These parameters are entered into the plugin as follows:

• Molecule: Select a structure, either by selecting a molecule already loaded in VMD, or by selecting the PSF and PDB files for a stored structure.
• Origin and Basis: If you just created this structure, the Origin and Basis parameters will be carried over from the Build Crystal task, otherwise, enter the Origin (center of the box) and the basis vectors for the periodic box.
• Grid spacing: The approximate resolution of the grid for deteriming the vacuum region. This is only an approximate parameter, since the actual distance is adjusted in each direction so that there are an integer number of grid points along each basis vector.
• Radius: A grid point is considered a vacuum if no atoms lie within the sphere of the specified radius around the grid point. Alternatively, atoms can be viewed as spheres of this radius, and a grid point is only a vacuum if it lies outside all the atoms.
• Shell thickness: The resulting surface shell will contain atoms within this distance of the surface.
• Shell file: The PSF/PDB files for the surface shell
• Interior file: The PSF/PDB files for the interior atoms

Click Find Shell to find the surface shell and interior structures, or Cancel to close the plugin window. This procedure may take a few minutes to complete.

Merge surface/interior atoms

This task lets you merge the surface and interior structures back into a single molecule after performing any desired processing on the individual parts.

• Surface/Interior Molecule: Select the two structures, either by selecting molecules already loaded in VMD, or by selecting the PSF and PDB files for the two stored structures.
• Material: The plugin uses the material type to get the parameter types used in the structure.
• Merged file: The PSF/PDB files for the reassembled structure

Click Merge to combine the two structures, or Cancel to close the plugin window.

Merge two molecules

This task lets you merge two structures, such as a device model and a biomolecule, into a single set of structure files. Both structures must have any desired bond information already encoded in the PSF files.

• Molecule 1/2: Select the two structures, either by selecting molecules already loaded in VMD, or by selecting the PSF and PDB files for the two stored structures.
• Merged file: The PSF/PDB files for the combined structure

Click Merge to combine the two structures, or Cancel to close the plugin window.

Solvate box

• Molecule: Select a structure, either by selecting a molecule already loaded in VMD, or by selecting the PSF and PDB files for a stored structure.
• Origin and Basis: If you just created this structure, the Origin and Basis parameters will be carried over from the Build Crystal task, otherwise, enter the Origin (center of the box) and the basis vectors for the periodic box.
• Solvated file: The PSF/PDB files for the resulting solvated structure

Click Solvate Box to solvate the structure, or Cancel to close the plugin window.

Beckman Institute for Advanced Science and Technology // National Institutes of Health // National Science Foundation // Physics, Computer Science, and Biophysics at UIUC
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