SIRAH

SIRAH converts and analyzes molecular dynamics (MD) simulations using coarse-grained (CG) models to reduce computational cost while preserving critical molecular interactions.

Key Features:

• Conversion Utilities: Transforms all-atom coordinates into arbitrary residue-based coarse-grained schemes.
• Topological Information Handling: Writes GROMACS topological data at any resolution into PSF format.
• Visualization and Analysis Plugin: Provides a VMD plugin to visualize, analyze, and extract pseudo-atomistic information from CG trajectories.
• Force Field Support: Provides explicit support for the SIRAH force field for coarse-grained simulations.
• Implementation Languages: Components are implemented in Perl, Tcl, and R.

Scientific Applications:

• Coarse-grained conversion: Enables conversion of all-atom MD data to residue-based CG representations for tailored simulations.
• Multi-resolution topology generation: Produces PSF files from GROMACS topologies at arbitrary resolutions for multi-scale workflows.
• CG trajectory analysis: Facilitates visualization, analysis, and extraction of pseudo-atomistic information from CG trajectories in VMD.
• SIRAH force field simulations: Supports application and analysis of simulations using the SIRAH force field to study molecular systems with reduced computational cost.

Methodology:

Conversion of all-atom coordinates to residue-based CG schemes; writing GROMACS topologies into PSF at arbitrary resolution; use of a VMD plugin to visualize, analyze, and extract pseudo-atomistic information from CG trajectories; components implemented in Perl, Tcl, and R.