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.
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.
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:
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.
You can minimize only a part of a molecule (a part of a connected component) by freezing the rest of the molecule:
The frozen (fixed) atoms are not minimized and their positions stay fixed.