Python scripts used to construct a coarse-grained (CG) amorphous silica AFM tip and to analyze AFM tip–lipid membrane interaction simulations performed using GROMACS and the MARTINI 3 force field.
Requirements:
Python3 or greater
MDAnalysis 2.6.1 or greater
Repository Structure:
AFMForceLipid/
├── AFM Tip/
│ ├── cgsilica.py # Build CG amorphous silica from atomistic structure
│ └── tipshaping.py # Generate a square pyramidal AFM tip geometry
├── Analysis/
│ ├── force_analysis.py # Analyze AFM tip force data (.xvg)
│ └── position_analysis.py # Analyze AFM tip position data (.xvg)
├── .gitattributes
├── LICENSE
├── README.md