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bioRxiv · 10.1101/2025.04.16.649160

TS2CG as a membrane builder

Schuhmann, F.·Stevens, J. A.·Rahmani, N.·Lindahl, I.·Brown, C. M.·Brasnett, C.·Anastasiou, D.·Bravo Vidal, A.·Geiger, B. J.·Marrink, S.-J.·Pezeshkian, W.
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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 Mobius strip membrane, a vesicle with lipid domain as continental plates (Martini globe), and entire mitochondrial membranes exhibiting lipid heterogeneity due to curvature, along with a comprehensive set of tutorials.

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Schuhmann, F., Stevens, J. A., Rahmani, N., Lindahl, I., Brown, C. M., Brasnett, C., Anastasiou, D., Bravo Vidal, A., Geiger, B. J., Marrink, S.-J., Pezeshkian, W.. 2025-04-17. TS2CG as a membrane builder. https://doi.org/10.1101/2025.04.16.649160

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