By Gregory A. Voth
This is often easily the easiest, most recent ebook within the box of coarse-graining proteins, lipids and different process of curiosity in biomolecular simulations. it's a e-book with chapters written in a transparent and available demeanour through experts that experience designed and demonstrated those tools themselves. it'd be particularly precious for younger researchers and graduate scholars that want an up-to-date advisor to coarse-graining approaches.
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Extra info for Coarse-Graining of Condensed Phase and Biomolecular Systems
1 are applications of the MS-CG method for modeling peptides [panel (b)] and monosaccharide solutions [panel (c)]. ) A schematic depicting various aspects of the MS-CG methodology for biomolecular systems. (a) The MS-CG method being applied for modeling interactions between lipids, cholesterol, and membrane-bound proteins, such as the N-BAR domain. The MS-CG method has been implemented with both explicit solvent (1) and solvent-free (2) CG models. The MS-CG method also applied for modeling peptides (b) and monosaccharide solutions (c).
In the CG configuration R N , the net force on CG site I from all CG sites that are within this distance range from site I is then Fd GI ;d ( R N ) = φ d GI ;d ( R N ), since the magnitude of the force from all CG sites J in that distance range is the same. 19) N ∑ ∑ ∑ (Rˆ IK ˆ ) δ ( R − R ) δ (R − R ′ ) .
Coarse-grained simulation of domain formation in an unsaturated/saturated (diC16:2/diC16 PC 1:3) phospholipid mixture. The saturated lipid is colored green, the unsaturated lipid purple. Upper snapshots: top view of the membrane showing only the second tail beads of the lipids. Large/small beads are used for tails in the gel/fluid phase. A darker shade is used for the underlying monolayer. At t = 0 the system was quenched from the fluid phase at T = 295 K into the gel–liquid coexistence region at T = 273 K.