Erik Lindahl

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$IMSL Math/Library Special Functions$

Lipid force fields • Groups: phosphate, choline, glycerol, acyl • Surprisingly hard to get accurate results • Many force fields lead to lipid area & volumes that are 20% lower than experimental values! • Do NOT use: Vanilla Gromacs FF, Gromos96, OPLS-AA/L, Amber, old Charmm FF • Do USE: Berger lipid force field, Charmm27 • Berger is available on Gromacs site, Charmm27 in beta for Gromacs distributions
Lipid topologies • No bilayer coordinates in PDB • No standardized atom or chain names • pdb2gmx does not work automatically • Best option: Find existing topologies (Gromacs site, Tieleman, <strong>Lindahl</strong>, others) • Alternative 1: Create RTP building blocks • Alternative 2: Hack topologies manually
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: Bilayer simulations • Lipid param
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 and 22: Coulomb interactions • Very large
Page 23 and 24: Pressure coupling • Two-dimension
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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