TS2CG as a Membrane Builder
Fabian Schuhmann, Jan A. Stevens, Neda Rahmani, Isabell Lindahl, Chelsea M. Brown, Christopher Brasnett, Dimitrios Anastasiou, Adrià Bravo Vidal, Beatrice J. Geiger, Siewert J. Marrink, Weria Pezeshkian
Abstract
Molecular dynamics (MD) simulations excel at capturing biological processes at the molecular scale but rely on a well-defined initial structure. As MD simulations now extend to whole-cell-level modeling, new tools are needed to efficiently build initial structures. Here, we introduce TS2CG version 2, designed to construct coarse-grained membrane structures with any desired shape and lateral organization. This version enables precise placement of lipids and proteins based on curvature preference, facilitating the creation of large, near-equilibrium membranes. Additional features include controlled pore generation and the placement of specific lipids at membrane edges for stabilization. Moreover, a Python interface allows users to extend functionality while maintaining the high performance of the C++ core. To demonstrate its capabilities, we showcase challenging simulations, including a Möbius strip membrane, a vesicle with lipid domains as continental plates (Martini globe), and entire mitochondrial membranes exhibiting lipid heterogeneity due to curvature, along with a comprehensive set of tutorials.