Quickly Find Structural Groups Based on Partial Charges in SAMSON

When working with large molecular systems, locating structural groups with specific charge distributions can be a tedious task. Whether you are investigating charge transfer, analyzing molecular interactions, or debugging unexpected electrostatic properties, you often need to filter and select structural groups based on their partial charges. Fortunately, if you’re using SAMSON’s Node Specification Language (NSL), there’s an efficient way to do this.

Why partial charges matter

In molecular simulations and modeling, partial charges represent how electrons are distributed among atoms in a molecule. These charges influence molecular properties such as solubility, dipole moments, and reactivity. For instance, in charge-sensitive systems like enzyme active sites or ionic crystals, identifying groups with high or low partial charges can help validate models, predict behavior, or prepare simulation input.

Using NSL to find structural groups with specific partial charges

SAMSON’s Node Specification Language supports searching for nodes by attribute values. For structural groups, this includes the partialCharge attribute (sg.pc for short).

The attribute sg.pc allows you to query structural groups with:

  • exact charge values, e.g., sg.pc 1
  • inequalities, e.g., sg.pc > 1.5
  • ranges, e.g., sg.pc 1.5:2.0

This provides a quick and expressive way to find groups that contribute significantly to the system’s electrostatics or to identify potentially anomalous regions in coarse-grained or detailed models.

Example scenarios

Here are a few example uses of sg.pc in your workflow:

  • Filtering highly polarized structural groups: Quickly isolate regions with unbalanced charges using sg.pc > 5.
  • Visual debugging: Highlight all groups with negative partial charge using sg.pc < 0—ideal for visual inspection of charge consistency.
  • Preparing simulations: Select only neutral groups with sg.pc 0 before launching an MD simulation step.

Combine filters

You can combine sg.pc with other structural group attributes for more refined queries. For example:

This finds structural groups that have a partial charge in the range 1.5 to 2.0 and more than 5 carbon atoms.

Performance tip

Using the short attribute name (e.g., sg.pc) instead of the full name (e.g., structuralGroup.partialCharge) not only keeps your queries more readable but also speeds up selection in larger scenes when used programmatically.

Try it yourself

To use these filters, simply type your query into the Search bar in SAMSON or use them as part of a script within your own workflows. Using NSL is a straightforward way to significantly improve your productivity when working with complex molecular scenes.

To learn more, visit the original documentation page on Structural Group Attributes.

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

Comments are closed.