Simulated Annealing Options Dialog Box

Simulated Annealing Options Dialog Box Features

• Rotation settings
  • Weight text box
  • Maximum rotation text box
• Translation settings
  • Weight text box
  • μ text box
  • σ text box
• Temperatures text box
• Iterations text box
• Energy terms options
  • Force field option and button
  • Gravity option and Scale factor text box
• Reset button

Rotation settings

These settings control the probability and size of rotation moves in the Monte Carlo simulation.

Weight text box

Relative probability of a rotation move in the Monte Carlo simulation, compared to a translation move. The rotation and translation weights do not need to add up to 1, as they are normalized before use.

Maximum rotation text box

Maximum size of a rotation move, in degrees. The random sampling to generate a rotation move is confined to the range specified.

Translation settings

These settings control the probability and size of translation moves in the Monte Carlo simulation. The translation moves are chosen using a log-normal probability distribution for the selection of the translation distance, and a random direction.

Note that the mean value of the log-normal distribution is exp(μ+σ²/2), so for the default values of μ and σ the mean distance would be about 2 Å.

Weight text box

Relative probability of a translation move in the Monte Carlo simulation, compared to a rotation move. The translation and rotation weights do not need to add up to 1, as they are normalized before use.

μ text box

Location parameter of the log-normal distribution used to choose a translation move. The median translation distance is exp(μ).

σ text box

Scale parameter of the log-normal distribution used to choose a translation move.

Temperatures text box

Temperatures in kelvin for the simulated annealing, given in order of application, separated by colons.

Iterations text box

Number of iterations (moves) to be performed at each temperature.

Energy terms options

Specify the energy terms used to decide whether a move is accepted. You can combine both energy terms to ensure that molecules don't get too close to each other while they are encouraged to move towards the substrate.

Force field option and button

Calculate the energy of the system using the selected force field. The system includes the substrate, if it is present. Click the Force Field button to select the force field, which is reported to the left of the button.

Gravity option and Scale factor text box

Calculate the energy of the system as a simple factor of the minimum distance between any atom in the molecule and any substrate atom (or the center of the box if there is no substrate), with the factor specified in the Scale factor text box. A hard-sphere model of the atoms is used to avoid clashes.

Reset button

Reset the options to their default values.