pyMBE: The Python-based molecule builder for ESPResSo

David Beyer

doi:10.1063/5.0216389

2024-07-12

PRE

David Beyer

Paola Beatriz Torres

Sebastián Pineda Pineda

Claudio F. Narambuena

Jean‐Noël Grad

Peter Košovan

Pablo M. Blanco *

DOI：10.1063/5.0216389

原文链接

摘要

En 中文

We present the Python-based Molecule Builder for ESPResSo (pyMBE), an open source software application 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 prone to mistakes, 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.

Keyword:

MONTE-CARLO

CHARGE REGULATION

ALPHA-LACTALBUMIN

PHASE-EQUILIBRIA

CHEMICAL-SHIFTS

FORCE-FIELD

SIMULATION

POLYELECTROLYTES

RESOLUTION