Lipid Bilayer Pressure Profile Calculation

Lipid Bilayer Pressure Profile Calculation

POPC bilayerProtein in lipid bilayer

Quick Review

http://en.wikipedia.org/wiki/Image:Phosphatidylcholine.png

Polar Head group

Hydrophobic interaction

Sterics & Entropy

Forces/Pressure in a bilayerMD Simulations

POPC

Minimization to reduce steric overlaps. (Gradient descent)

Heating and Equilibration at NPT. (raise from 0 to 310 K)

Pressure Profile Calculation at NVT

Schulten DLPE

Schulten POPC

Incorrect results (with vmd-generated POPC bilayer)

Charges are the problem?

Initial configuration: Very ordered (POPC bilayer made using vmd plugin)

Side view

Top view

Ordering direction hinted in red

Known Problems(vmd POPC bilayer)

Bilayer Imbalance

Periodic Boundary Condition

Cell volume during equilibration

Gap in the periodic display disappears after equilibration

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

Results: vmd POPC with fixed charges

Schulten POPC

Generating A POPE Membrane manually: Before minimization

Extra kinked lipid No kink lipid

VMD pope templateGenerated pope template

Are the Charges OK?

VMD POPE membrane

Generated Membrane

POPE

(minimized)