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You can minimize your structures interactively in SAMSON. To start and stop the minimization click Edit menu > Minimize (shortcut: Z ).

The interactive minimization uses the Universal Force Field (UFF).

During the minimization you can:

You can modify the interactive minimizer options in the Minimize section in the Preferences panel.

The interactive minimization preferences

By default, the minimizer minimizes all the molecules in the active document.

What you will learn from this tutorial

From this tutorial, you will learn:

What is not covered in this tutorial

For how to simulate systems please refer to the Modeling and Simulation section.

Minimizing a single molecule in a document

Prerequisites: Please refer to the Selecting section to learn how to select objects in SAMSON.

If you would like to minimize only a single molecule (a single connected component) in a document without minimizing other molecules in the system, then:

  1. Uncheck the "Include all atoms in the document" option in Preferences > Editors > Minimize
  2. Select a molecule that you would like to minimize.
  3. Click Edit menu > Minimize (shortcut: Z ).

Note: When minimizing a selection only, the minimizer takes into account the whole connected component of the current selection, i.e. if you choose a single atom in a molecule, then it will take into consideration the whole molecule connected to this atom and will minimize this whole connected component. If you would like to minimize only a part of a molecule, then please refer to the Minimizing a part of a molecule section.

Minimizing a part of a molecule

You can minimize only a part of a molecule (a part of a connected component) by freezing the rest of the molecule:

  1. Select the whole molecule or keep the selection empty.
  2. Click Edit menu > Freeze to freeze (fix) atoms in the selection or in the whole document if the selection is empty.
  3. Select the part of the molecule that you would like to minimize.
  4. Click Edit menu > Unfreeze to unfreeze only atoms in the selection.
  5. Click Edit menu > Minimize to start the interactive minimization.
  6. ...
  7. Click Edit menu > Minimize to stop the interactive minimization.
  8. Unfreeze the whole system by clicking Edit menu > Unfreeze with the molecule selected or nothing selected.

The frozen (fixed) atoms are not minimized and their positions stay fixed.