The Group of Biomolecular Simulations at the Institut Pasteur de Montevideo (@IPMontevideo ), and the National Supercomputing Center (@ClusterUy ) launched the SIRAH-CoV2 initiative. https://t.co/NKBLpqQrmQ
— SIRAH Forcefield (@SIRAHForcefield) April 13, 2020
ABOUT SIRAH
SIRAH is a coarse-grained and multiscale force field for molecular dynamics simulations that offers plug-and-play topologies and parameters for aqueous solvent, phospholipids, DNA, metal ions, and proteins, including post-translational modifications and glycosylation.
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 includes:
- A description of different protonation states and most common post-translational modifications for protein residues;
- Compatibility for mapping various 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 latest version of SIRAH is available at SIRAH FF GitHub:
SIRAH GITHUBSteps to perform a SIRAH simulation
CG simulations with the SIRAH force field inherited setups, formats, atom types, partial charges, and other parameters from standard atomistic MD simulations. Consequently, anyone familiar with GROMACS, AMBER, or NAMD can easily perform a SIRAH CG simulation.
1. Download SIRAH
Download SIRAH at SIRAH GitHub and uncompress the *.tgz file
2. Check your coordinate file
Add all hydrogens following the correct protonation states of each residue at a given pH
3. Map AA to CG
Map an all-atom coordinate file to CG representantion with the SIRAH Tool's cgconv.pl script
4. Build Topologies
Build the topology of your system using Ambertools or GMX tools just like standard atomistic MD simulations
5. Run
Run your CG sytem with with AMBER, GROMACS, or NAMD
6. Analyze
Analyze your simulation with VMD and the SIRAH Tools plugin in VMD
Check out the SIRAH Tutorials!
You can learn how to use SIRAH in AMBER, GROMACS, and NAMD by reading the helpful tutorials on the SIRAH documentation page.
There are also tutorials on how to use SIRAH Tools and do trajectory analysis with VMD.