pysimm

pysimm provides Python-based capabilities to generate, modify, and simulate molecular systems for computational chemistry and bioinformatics studies, including molecular dynamics and amorphous polymer simulations.

Key Features:

• Structure Generation: Generates complex molecular structures and enables design and manipulation of molecular configurations.
• Simulation Tools: Provides simulation utilities for molecular dynamics and analysis of molecular interactions.
• Modification Capabilities: Enables modification of existing molecular systems to study structural changes and their effects on molecular behavior.
• Integration with Third-Party Software: Interfaces with other optimized software to extend simulation workflows and functionality.

Scientific Applications:

• Amorphous Polymer Simulations: Supports simulation and methodological development focused on amorphous polymers.
• Method Development: Facilitates rapid development of new methodologies for molecular simulation studies.

Methodology:

Pysimm employs abstraction layers that standardize the assignment of various force field models to molecular systems.