Klauda Lab Simulation Wiki

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[[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]]