DynaMate: leveraging AI-agents for customized research workflows

Developments related to large language models (LLMs) have deeply impacted everyday activities and are even more significant in scientific applications. They range from simple chatbots that respond to a prompt to very complex agents that plan, conduct, and analyze experiments. As more models and algorithms continue to be developed at a rapid pace, the complexity involved in building this framework increases. Additionally, editing these algorithms for personalized applications has become increasingly challenging. To this end, we present a modular code template that allows easy implementation of custom Python code functions to enable a multi-agent framework capable of using these functions to perform complex tasks. We used the template to build DynaMate, a complex framework for generating, running, and analyzing molecular simulations. We performed various tests that included the simulation of solvents and metal–organic frameworks, calculation of radial distribution functions, and determination of free energy landscapes. The modularity of these templates allows for easy editing and the addition of custom tools, which enables rapid access to the many tools that can be involved in scientific workflows.