CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers

Area of Science:

• Polymer Science and Engineering
• Computational Chemistry
• Materials Science

Background:

• Molecular modeling and simulations are crucial for understanding polymer properties and mechanisms.
• Creating realistic polymer models is complex due to structural diversity and scale variations.
• Existing methods require significant expertise and time.

Purpose of the Study:

• To introduce Polymer Builder, a web-based tool within CHARMM-GUI for automated polymer system construction.
• To provide a generalized and versatile platform for building complex polymer structures and simulating melts/solutions.
• To validate the tool's capabilities through various polymer system simulations.

Main Methods:

• Development of a web-based infrastructure, Polymer Builder, integrated with CHARMM-GUI.
• Implementation of versatile modeling methods for complex polymer structures.
• Generation of polymer melt and solution systems using coarse-grained models and all-atom replacement.
• Extensive validation of coarse-grained model parametrization against experimental data and all-atom simulations.

Main Results:

• Demonstrated capability in generating relaxed polymer systems.
• Successful density calculations for 34 homopolymer melt systems.
• Characteristic ratio calculations for 170 homopolymer melt systems.
• Generated morphology diagrams for block copolymers and simulated self-assembly behavior.

Conclusions:

• Polymer Builder offers a generalized and automated approach to polymer system construction.
• The tool facilitates advanced molecular modeling and simulation research in polymer science.
• It enables deeper insights into the structures, dynamics, and mechanisms of complex polymer systems.