When working on complex molecular systems, it’s common to want to optimize the geometry of just one molecule without affecting the rest of the scene. But doing this selectively — without unintentionally altering neighboring structures — can be tricky.
SAMSON offers a straightforward solution to this by allowing users to minimize specific molecules (or connected components) within larger molecular documents. This feature can be incredibly useful when dealing with multi-molecular assemblies where localized refinement is needed before running more resource-intensive simulations.
Why minimize a single molecule?
Imagine you’re preparing a heterogeneous system with different molecules, and you’ve just added or edited one molecule. Running a full system optimization might displace or alter other carefully-positioned structures. In these cases, minimizing a single molecule — while keeping everything else as is — can save both time and structural accuracy.
Three simple steps to target just one molecule
Minimizing a single component in SAMSON requires just a couple of clicks once you understand the settings and selection logic:
- Go to Interface > Preferences > Editors > Minimize, and uncheck the option Include all atoms in the document. This tells SAMSON not to apply the minimization to everything by default.
- Select the specific molecule (or connected component) you wish to refine. You can do this using the selection tools as described in this guide.
- Activate minimization via Edit > Minimize or by pressing the keyboard shortcut Z.
This process applies the interactive minimizer using the Universal Force Field (UFF) only to the selected component, leaving other molecules untouched. It’s ideal for local tweaks or when preparing parts of a system iteratively.
Note
When you select just part of a molecule, SAMSON automatically identifies the entire connected component. So even if you only click on one atom, the entire covalently bonded structure will be optimized. To minimize only a portion of a molecule, you’d need to use the freezing method described in more advanced sections.
Visual Settings
Minimization behaviors and force field parameters can be customized in the preferences panel, giving you flexibility over how atoms are treated during interactive refinement.
This targeted minimization approach can be especially helpful for researchers adjusting ligands in a binding pocket, refining molecular fragments, or performing stepwise optimizations during model building.
To learn more about molecule minimization and related tools in SAMSON, visit the full documentation: https://documentation.samson-connect.net/users/latest/minimizing/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.