Erik Lindahl

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$IMSL Math/Library Special Functions$

Van der Waals stuff • One reason for the difficulties in simulating membranes is the sensitivity to nonbonded Van der Waals parameters • Small changes will affect packing of chains, and thus the pressure and area/lipid • Normal cut-off or switch around 1.0nm is OK, but turn on long-range dispersion correction to get correct pressure
Pressure coupling • Two-dimensional liquid crystals • Bilayer should be able to deform in XY-plane • Anisotropic pressure coupling should be enabled throughout production runs! • Neat trick: Semiisotropic coupling (XY+Z) • Berendsen coupling does not provide a true NPT ensemble - Parinello-Rahman is better • Slow relaxation (10ps) to avoid oscillations
Page 1 and 2: Simulations of Membranes & Membrane
Page 3 and 4: Importance of Membranes • Control
Page 5 and 6: Lipid names... • DPPC - Dipalmito
Page 7 and 8: Bilayer phases • Very low tempera
Page 9 and 10: A liquid crystalline bilayer
Page 11 and 12: Bilayer simulations • Lipid param
Page 13 and 14: Lipid topologies • No bilayer coo
Page 15 and 16: Example DPPC topology ... [ dihedra
Page 17 and 18: Bilayer structures • Find pre-equ
Page 19 and 20: Cell shapes • Rectangular membran
Page 21: Coulomb interactions • Very large
Page 25 and 26: Thermostats • Polar and non-polar
Page 27 and 28: Lipid diffusion • Frequently over
Page 29 and 30: Order parameters • g_order (requi
Page 31 and 32: Example: cholesterol (Cells can con
Page 33 and 34: Membrane proteins • Prepare struc
Page 35 and 36: Mixed lipid & protein FFs • Berge
Page 37 and 38: Bilayer solvation in vivo hydrophob
Page 39: Summary • Easier than proteins: 2

Erik Lindahl

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