  We present the Python-based Molecule Builder for ESPResSo (pyMBE), an open
source software to design custom Coarse-Grained (CG) models, as well as
pre-defined models of polyelectrolytes, peptides and globular proteins in the
Extensible Simulation Package for Research on Soft Matter (ESPResSo). The
Python interface of \espresso offers a flexible framework, capable of building
custom CG models from scratch. As a downside, building CG models from scratch
is error-prone, especially for newcomers in the field of CG modeling, or for
molecules with complex architectures. The pyMBE module builds CG 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. To demonstrate some of the applications of
pyMBE, we showcase several case studies where we successfully reproduce
previously published simulations of charge-regulating peptides and globular
proteins in bulk solution and weak polyelectrolytes in dialysis. The pyMBE
module is publicly available as a GitHub repository
(https://github.com/pyMBE-dev/pyMBE) which includes its source code and various
sample and test scripts, including the ones that we used to generate the data
presented in this article.
