Freezing Atoms to Fine-Tune Molecular Geometry

When performing molecular modeling, it’s common to want to optimize only a specific part of a molecule while keeping the rest unchanged—for example, when adjusting a binding site or relaxing a region around a mutation. However, many molecular modelers run into the problem of traditional minimization altering the entire structure, leading to results that are difficult to interpret or which invalidate parts of the carefully-built model.

SAMSON offers a practical way to deal with this through partial minimization using atom freezing. This approach lets you freeze part of the molecular structure and minimize only the section you want to modify. This post walks you through how to do that in SAMSON, using its interactive minimization capabilities.

Why freeze atoms?

Selective minimization is useful in many scenarios:

  • Relaxing local regions near edits (e.g., point mutations or docking sites)
  • Preserving experimental geometries while allowing local relaxation
  • Maintaining known structural motifs or active sites

How partial minimization works

SAMSON allows you to designate certain atoms as “frozen”. These atoms will not be moved during energy minimization, allowing you to adjust only selected areas. Here’s how to do it:

  1. Select everything you want to keep fixed (or nothing, if you want to freeze the entire structure).
  2. Click Edit > Freeze. This freezes those atoms.
  3. Select the part of the molecule you want to minimize.
  4. Click Edit > Unfreeze to unfreeze just that part.
  5. Click Edit > Minimize to begin interactive minimization.
  6. Watch the geometry update in real-time as the minimizer runs.
  7. Click Edit > Minimize again to stop the process.
  8. When finished, click Edit > Unfreeze again to unfreeze everything.

Frozen atoms are shown with a dark blue overlay in the SAMSON viewport, so you always know which parts remain static. This feature is especially useful in complex models where visual cues are essential during editing.

The interactive minimization preferences

Tips and reminders

  • If you’re minimizing just a few atoms within a chain or ring, remember the minimizer will still consider the full connected component unless frozen explicitly.
  • The shortcut Z can be used to start or stop a minimization quickly.
  • Minimization settings can be adjusted in Interface > Preferences > Editors > Minimize.

Below is an example video showing how a specific part of a molecule is minimized while other regions remain fixed:

To learn additional techniques for working with force fields and minimization in SAMSON, you can explore the full documentation at the link below.

Read the full documentation on structure minimization in SAMSON.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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