pyMBE: the Python-based Molecule Builder for ESPResSo

What is it about?

We announce the first release of pyMBE, an open-source Python package designed to facilitate the design of custom coarse-grained models of polyelectrolytes, peptides and proteins in the software for molecular dynamics, ESPResSo. pyMBE extends the ESPResSo API with methods to automate repetitive and error-prone tasks, such as setting up chemical bonds, non-bonded interactions and reaction methods.

Featured Image

Photo by ANIRUDH on Unsplash

Photo by ANIRUDH on Unsplash

Why is it important?

Building CG models from scratch is prone to mistakes, especially for newcomers in the field of coarse-grained modeling, or for molecules with complex architectures. The pyMBE module builds coarse-grained models in ESPResSo using a hierarchical bottom-up approach, providing a robust tool to automate the setup of CG models and helping new users prevent common mistakes. ESPResSo features the constant pH (cpH) and grand-reaction (G-RxMC) methods, which have been designed to study chemical reaction equilibria in macromolecular systems with many reactive species. However, setting up these methods for systems which contain several types of reactive groups is an error-prone task, especially for beginners. The pyMBE module enables the automatic setup of cpH and G-RxMC simulations in ESPResSo, lowering the barrier for newcomers and opening the door to investigate complex systems not studied with these methods yet.

Perspectives