Bruininks Bart M H, Souza Paulo C T, Marrink Siewert J
Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
Methods Mol Biol. 2019;2022:105-127. doi: 10.1007/978-1-4939-9608-7_5.
Martini is a coarse-grained (CG) force field suitable for molecular dynamics (MD) simulations of (bio)molecular systems. It is based on mapping of two to four heavy atoms to one CG particle. The effective interactions between the CG particles are parametrized to reproduce partitioning free energies of small chemical compounds between polar and apolar phases. In this chapter, a summary of the key elements of this CG force field is presented, followed by an example of practical application: a lipoplex-membrane fusion experiment. Formulated as hands-on practice, this chapter contains guidelines to build CG models of important biological systems, such as asymmetric bilayers and double-stranded DNA. Finally, a series of notes containing useful information, limitations, and tips are described in the last section.
马蒂尼是一种粗粒度（CG）力场，适用于（生物）分子系统的分子动力学（MD）模拟。它基于将两到四个重原子映射到一个CG粒子。CG粒子之间的有效相互作用经过参数化处理，以重现小化合物在极性和非极性相之间的分配自由能。在本章中，将对这种CG力场的关键要素进行总结，随后给出一个实际应用示例：脂质体-膜融合实验。作为实践操作内容，本章包含构建重要生物系统（如不对称双层膜和双链DNA）的CG模型的指南。最后，在最后一节中描述了一系列包含有用信息、局限性和提示的注释。
