dimer-builder-step 2026.7.6

A SEAMM plug-in for Dimer Builder

SEAMM Dimer Builder Plug-in

A SEAMM plug-in for Dimer Builder

• Free software: BSD-3-Clause

• Documentation: https://molssi-seamm.github.io/dimer_builder_step/index.html

• Code: https://github.com/molssi-seamm/dimer_builder_step

Features

• Please edit this section!

Acknowledgements

This package was created with the molssi-seamm/cookiecutter-seamm-plugin tool, which is based on the excellent Cookiecutter.

Developed by the Molecular Sciences Software Institute (MolSSI), which receives funding from the National Science Foundation under award CHE-2136142.

History

2026.7.6 – Energy-based contact and GUI refinements

• Added an energy contact method: with a Model Chemistry step before the Dimer Builder step, the contact distance is found from the energy minimum along each approach direction (falling back to the van der Waals estimate for orientations with no binding well). It uses the new seamm_mdi MDI driver to evaluate the energy, and reports which model chemistry was used and how many times it was called.

• Configuration names now use a comma (e.g. 2,1) rather than a slash, which is reserved for separating system and configuration names.

• The dialog no longer shows the unused Flowchart tab, and reminds you to add a Model Chemistry step when the energy contact method is chosen and none precedes this step.

2026.6.30 – Initial release

• Generates sets of dimer (molecule-pair) configurations across a range of separations and relative orientations, for building interaction-energy data sets and training sets for machine-learned force fields.

• Two ways to provide the input structures:

  • two sets of monomer conformers, which are assembled into dimers at random relative orientations; or

  • prepared complexes, each scanned along the axis between a “fixed” and a “movable” group (taken from subsets if present, otherwise the last molecule is movable and the rest are fixed).

• For each orientation, scans the center-to-center separation from just inside the van der Waals contact distance out to a chosen maximum, with geometric (default), linear, or explicit spacing.

• Records the scan geometry on every configuration as properties – separation, gap beyond contact, the approach-direction angles, and the movable group’s orientation angles – and marks the two molecules as “fixed” and “movable” subsets, so the pieces are easy to find downstream.

• Stores all the generated structures as conformers of a new system, named by orientation and point (1/1, 1/2, …) by default.