SIRAH is a coarse-grained force field for molecular dynamics simulations that offers plug-and-play topologies and parameters for aqueous solvent, phospholipids, DNA, metal ions, and proteins. It was designed, implemented, and developed by the Biomolecular Simulations Group at the Institut Pasteur de Montevideo, Uruguay, which is also responsible for its regular maintenance.
The current version, SIRAH 2.0, includes:
- A series of modifications to both bonded and non-bonded parameters of amino acids while preserving their original topologies;
- A description of different protonation states and post-translational modifications for protein residues;
- An improvement in compatibility for mapping different force field atom types and experimental structures;
- The ability to leverage GPU acceleration in AMBER and GROMACS codes;
- A collection of scripts, known as SIRAH Tools, that facilitate the process of mapping all-atom files to CG representations, backmapping, visualizing, and analyzing SIRAH trajectories directly on the popular VMD program for molecular visualization.
The present project is undergoing continuous development.