bilayer_simulations
Bilayer Analysis Instructions
Here are a list of instructions for properties you may want to compute:
Surface Area of Lipid
(overall)
Equilb Test
and Area Compressibility
Comp-SA
(surface area of each lipid component)
SCD
(chain order parameters)
EDP
(electron density profiles)
Tilt Angle
(sterol)
2D RDFs
Hydrogen Bonds for Single-Component Bilayers
Hydrogen Bonds for Multi-Component Bilayers
(lipids and sterol)
Lipid Wobble
(cross-chain)
Lipid Clustering
Pairwise 2D-RDF and Clustering
Packing Defects
Chain Interdigitation
Dipole Potential and ESP
Drug or Peptide distance to bilayer
1D (Z) NAMD Potential of Mean Force
Psi/Phi Mapping and Alpha Beta Helix
Interaction Energy of Ligand in Charmm
RMSD
Adjusting Water Level and Mutating Residues of Existing Simulations