Supporting scripts and data for "Martini3-IDP: Improved Martini 3 Force Field for Disordered Proteins"

DEPRECATION UPDATE JULY 2025

The contents of this repository has been fully integrated into both Vermouth-Martinize and Polyply. The tutorials detailed in force_field/readme.md are deprecated. In both programs, the force field described in the files here and the associated publication can be specified using -lib martini3idp (polyply) or -ff martini3idp (martinize2). If you encounter problems with either implementation, open an issue in the respective repository.

In the case of martinize2, the program now handles disordered regions using the -id-regions and -idr-tune flags. No customised version of Vermouth-Martinize is necessary to annotate these regions as previously described, and is strongly discouraged.

Reference

Wang, L., Brasnett, C., Borges-Araújo, L. et al. Martini3-IDP: improved Martini 3 force field for disordered proteins. Nat Commun 16, 2874 (2025). https://doi.org/10.1038/s41467-025-58199-2

Martini3-IDP force field parameters and all related data/scripts.

• structure data for most simulations from the paper are available here

• Martinize2 and Polyply format force field files are available in the force_field folder

• User tutorials are available here

• Detailed processed data and python scripts of each testing are provided under corresponding folder