Klauda Lab Simulation Wiki

Here are a list of instructions for properties you may want to compute:

1. Surface Area of Lipid (overall)
2. Equilb Test and Area Compressibility
3. Comp-SA (surface area of each lipid component)
4. SCD (chain order parameters)
5. EDP (electron density profiles)
6. Tilt Angle (sterol)
7. 2D RDFs
8. Hydrogen Bonds for Single-Component Bilayers
9. Hydrogen Bonds for Multi-Component Bilayers (lipids and sterol)
10. Lipid Wobble (cross-chain)
11. Lipid Clustering
12. Pairwise 2D-RDF and Clustering
13. Packing Defects
14. Chain Interdigitation
15. Dipole Potential and ESP
16. Drug or Peptide distance to bilayer
17. 1D (Z) NAMD Potential of Mean Force
18. Psi/Phi Mapping and Alpha Beta Helix
19. Interaction Energy of Ligand in Charmm
20. RMSD
21. Adjusting Water Level and Mutating Residues of Existing Simulations