dimer-builder-step 2026.6.30

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

2026.6.30 – 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.