GROMACS-SWAXS

Welcome to GROMACS-SWAXS, a modified GROMACS version for:

• predictions of small-angle X-ray and neutron scattering (SAXS/SANS) curves from explicit-solvent MD simulations,

• structure refinement of proteins or soft-matter complexes against SAXS/SANS curves

Documentation

• Usage
  • Modified and added GROMACS modules
  • gmx mdrun input options
  • gmx mdrun output
  • mdp options
  • Environment variables
  • References
• Installation
  • Prerequisites
  • Downloading
  • Building
  • Running
  • Troubleshooting
  • The last resort
• Tutorials
  • GB3 domain how-to for MD beginners
  • Computing a SAXS curve, a step by step guide
  • SAXS/SANS predictions, SAXS-driven MD, and multi-replica ensemble refinement
  • SAXS and SANS curves of a protein-detergent complex
• Force-fields
  • Top force field file forcefield.itp
  • Water and ion itp files
  • Available force-fields
• Getting help
• References
  • Overview articles
  • SAXS/WAXS/SANS curve predictions from MD simulations
  • SAXS/WAXS/SANS-driven MD simulations
  • SAXS-guided maximum-entropy ensemble refinement
  • Applications

This software is developed by the Computational Biophysics group at Saarland University.

References are listed in Usage.