Lipid Bilayer Pressure Profile Calculation
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Transcript of Lipid Bilayer Pressure Profile Calculation
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Lipid Bilayer Pressure Profile Calculation
POPC bilayerProtein in lipid bilayer
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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
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Schulten DLPE
Schulten POPC
Incorrect results (with vmd-generated POPC bilayer)
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Charges are the problem?
Initial configuration: Very ordered (POPC bilayer made using vmd plugin)
Side view
Top view
Ordering direction hinted in red
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Known Problems(vmd POPC bilayer)
Bilayer Imbalance
Periodic Boundary Condition
Cell volume during equilibration
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Gap in the periodic display disappears after equilibration
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After Equilibration, vmd POPC bilayer with charges fixed (at first)
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Results: vmd POPC with fixed charges
Schulten POPC
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Generating A POPE Membrane manually: Before minimization
Extra kinked lipid No kink lipid
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VMD pope templateGenerated pope template
Are the Charges OK?
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VMD POPE membrane
Generated Membrane
POPE
(minimized)