Paper Citing NAMD - Abstract
Wang, Zun-Jing; Deserno, Markus
A Systematically Coarse-Grained Solvent-Free Model for Quantitative Phospholipid Bilayer Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:11207-11220, SEP 2 2010
We present an implicit solvent coarse-grained (CG) model for quantitative simulations of 1-palmitoyl-2oleoyl-sn-glyeero-3-phosphocholine (POPC) bilayers The absence of explicit solvent enables membrane simulations on large length and time scales at moderate computational expense. Despite improved computational efficiency, the model preserves chemical specificity and quantitative accuracy The bonded and nonbonded interactions together with the effective cohesion mimicking the hydrophobic effect were systematically tuned by matching structural and mechanical properties from experiments and all-atom bilayer simulations, such as saturated area per lipid, radial distribution functions, density and pressure profiles across the bilayer, P-2 order, etc The CG lipid model is shown to self-assemble into a bilayer starting from a random dispersion Its line tension and elastic properties, such :Is bending and stretching modulus, are semiquantitatively consistent with experiments. The effects of (i) reduced molecular friction and (ii) more efficient integration combine to an overall speed-up of 3-4 orders of magnitude compared to all-atom bilayer simulations Our CG lipid model is especially useful for studies of large-scale phenomena in membranes that nevertheless require a fair description of chemical specificity, c g, membrane patches interacting with movable and transformable membrane proteins and peptides.
