pyPolyBuilder

pyPolyBuilder generates molecular topologies and initial configurations for classical molecular dynamics of arbitrary supramolecules, including linear polymer chains and branched structures such as dendrimers.

Key Features:

• Versatility: Generates topologies for a wide range of supramolecular systems beyond traditional biomolecules, including large branched molecules and dendrimers.
• Automation: Automates creation of molecular topology files for complex molecular structures to streamline simulation setup.
• Starting Structure Generation: Produces reasonable initial configurations suitable for classical molecular dynamics simulations.
• Implementation and Compatibility: Implemented in Python and designed for compatibility with multiple molecular simulation engines.

Scientific Applications:

• Nonbiological supramolecular modeling: Preparation of topologies and starting structures for supramolecular systems that are not well served by biomolecular tools.
• Materials science: Enabling molecular dynamics studies of polymeric and supramolecular materials to investigate their properties.
• Nanotechnology: Modeling branched and dendritic nanostructures for simulation-based characterization.
• Polymer chemistry: Supporting simulations of linear polymer chains and complex branched polymers such as dendrimers.

Methodology:

Implemented in Python and automates generation of molecular topology files and reasonable starting configurations for classical molecular dynamics, with outputs compatible with multiple simulation engines.