lipid bilayer pressure profile calculation
DESCRIPTION
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. - PowerPoint PPT PresentationTRANSCRIPT
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)