A Guide to Titratable Martini Simulations

The Martini force-field for molecular dynamics (MD) simulations is suitable for running MD simulations of complex bio(molecular) systems and nano-materials. Recently, titratable Martini was developed, which is an extension of the popular force-field that is suitable for running constant pH simulations within the Martini framework. In this chapter, the key concepts behind the titratable Martini model are summarized, followed by a tutorial style presentation of three application cases. These application cases demonstrate how to generate coordinates, run titration simulations, and analyze them with the help of the martini_sour package. Martini_sour is a dedicated Python suite for facilitating all aspects of titratable Martini simulations. Finally, a series of notes containing useful information, limitations, and tips are described in the last section.