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Lipid Bilayer Pressure Profile Calculation

Lipid Bilayer Pressure Profile Calculation. Protein in lipid bilayer. POPC bilayer. Quick Review. Forces/Pressure in a bilayer. MD Simulations. Polar Head group. Minimization to reduce steric overlaps. (Gradient descent). Hydrophobic interaction.

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Lipid Bilayer Pressure Profile Calculation

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  1. Lipid Bilayer Pressure Profile Calculation Protein in lipid bilayer POPC bilayer

  2. Quick Review Forces/Pressure in a bilayer MD Simulations Polar Head group Minimization to reduce steric overlaps. (Gradient descent) Hydrophobic interaction Heating and Equilibration at NPT. (raise from 0 to 310 K) Pressure Profile Calculation at NVT Sterics & Entropy POPC http://en.wikipedia.org/wiki/Image:Phosphatidylcholine.png

  3. Incorrect results (with vmd-generated POPC bilayer) Schulten POPC Schulten DLPE

  4. Initial configuration: Very ordered (POPC bilayer made using vmd plugin) Side view Charges are the problem? Top view Ordering direction hinted in red

  5. Known Problems (vmd POPC bilayer) Periodic Boundary Condition Bilayer Imbalance Cell volume during equilibration

  6. Gap in the periodic display disappears after equilibration

  7. After Equilibration, vmd POPC bilayer with charges fixed (at first)

  8. Results: vmd POPC with fixed charges Schulten POPC

  9. Generating A POPE Membrane manually: Before minimization Extra kinked lipid No kink lipid

  10. Are the Charges OK? Generated pope template VMD pope template

  11. Generated Membrane POPE (minimized) VMD POPE membrane

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