SMOG

SMOG generates structure-based models of biomolecules for molecular dynamics simulations, producing coarse-grained and all-atom simplified Hamiltonians derived from energy landscape theory and formatted for GROMACS.

Key Features:

• GROMACS integration: Produces model files and parameters formatted for use with the GROMACS molecular dynamics package.
• Structure-based modeling: Implements structure-based models derived from energy landscape theory of protein folding.
• Coarse-grained and simplified Hamiltonians: Supports coarse-grained and other simplified Hamiltonian formulations for reduced-complexity simulations.
• Versatile input compatibility: Accepts multi-chain biomolecular systems in PDB format including standard RNA, DNA, and amino acids.
• Output generation: Generates all necessary files required to implement the selected structure-based model within GROMACS.
• Model variants: Provides both C(alpha) and all-atom versions of structure-based models.

Scientific Applications:

• Large-scale dynamics: Investigation of biomolecular dynamics at large length scales and long time frames.
• Functional motions: Capture of functionally important motions in proteins and RNAs.
• Conformational processes: Study of protein folding, conformational changes, and molecular interactions.

Methodology:

Models are derived from energy landscape theory to construct structure-based coarse-grained and simplified Hamiltonian models and are exported as GROMACS-compatible files.