Disorder Options Dialog Box

Specify options relating to the initial placement of the molecules in the cell, rebuilding molecules, and some general options.

  • Features
  • Additional Resources

Disorder Options Dialog Box Features

Steric pack option

Maximize the density of the system by moving the structures towards the substrate (if one is defined) or the center of the cell, while avoiding steric clashes. Options for the van der Waals scaling for defining clashes, the initial density, and the number of attempts at placement are available in this dialog box and the Disorder tab of the Disordered System Builder Panel. Only available when Snapped to grid or Amorphous is chosen as the Initial state.

Once the structures are distributed in the cell, starting at the center or the surface and moving outward or upward, each structure is moved as a rigid body toward the origin along the vector between the molecular center and the origin. The point closest to the origin that causes no steric collisions is the new location of the structure. No rotation is performed and no other movement is performed. Structures are allowed to pass through each other to find the closest-to-the-origin cavity along the vector. Atoms are considered hard spheres and any overlap is considered a steric collision.

Monte Carlo simulated annealing option and Options button

Perform a Metropolis Monte Carlo simulated annealing calculation to minimize the energy of the system. The translation and rotation moves, temperatures, iterations, and energy terms to use can be set in the Simulated Annealing Options Dialog Box, which you open by clicking the Options button. The structure is moved as a rigid body. Only available when Snapped to grid or Amorphous is chosen as the Initial state.

Minimization option

Minimize the final configuration of the system using the specified force field. All the structures placed in the system are minimized, no longer being treated as rigid bodies.

Force Field button

Click the Force Field button to specify the force field to use and any custom charges, in the Force Field Dialog Box. The current force field is shown to the left of the button. Learn more about available force fields in the OPLS Force Fields and Machine Learning Force Fields documentation.

Maximize density option

Maximize the density of the system. If a system without clashes is found at the initial density, the density is increased until a system without clashes can no longer be found. This option is only available if the Keep constant option is VdW scale factor. It is also not available if a substrate of type Container is used, as the density is fixed by the number of molecules and the volume of the container.

Dihedral angle distribution options

Select an option for the probability distribution for sampling dihedral angles in the self-avoiding random walk algorithm for tangled chain rebuilding:

  • Uniform—sample dihedral angles using a uniform probability distribution.

  • Boltzmann at T K—sample dihedral angles using probabilities derived from a Boltzmann distribution of the dihedral angles at the specified temperature. The potential energy surface used for the Boltzmann distribution is calculated using the listed force field, which can be changed by clicking the Force Field button. A truncated version of the molecule being built is used for the potential energy surface, with sufficient atoms near the bond being added to provide a realistic surface. A lower temperature often yields better order along the chain and more extended molecules.

Placement attempts per molecule text box

Specify the maximum number of attempts to be made when placing a molecule in the cell. In each attempt, the molecule is oriented at random and placed in the cell at random. If a clash is detected, the attempt is regarded as failed, and a new attempt is made. If the maximum number of attempts is exceeded, the cell is discarded and a new cell is built. Only available when Amorphous or Tangled Chain is chosen as the Initial state.

Attempts per density/VdW scale text box

Specify the maximum number of attempts at building a cell. If a non-clashing cell cannot be built in this number of attempts, the density is lowered or the van der Waals scaling factor is lowered, depending on the Keep constant option. The process continues until a non-clashing cell can be built, or the density or scale factor are very small. Only available when Amorphous or Tangled Chain is chosen as the Initial state.

Rotational disorder option

Select this option to randomize the orientation of the molecules that are placed on a grid of points. If this option is deselected, the input orientation is used. Only used with the Snapped to grid initial state option.

Set random number seed option and text box

Select this option to specify a random seed for all random processes used in building the disordered structure. Specifying the seed allows you to reproduce the results, unless other factors affect them. If this option is not selected, a seed is chosen at random.

Reset button

Reset the options to their default values.

Okay button

Confirm the selections made in the dialog box.

Help button

Click to open the help topic for this dialog box.

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