Mapping between atomistic and CG models of PA-66. The circles denote which atoms are joined into CG beads. The designations of the beads are indicated by the labels.
Scheme of the backmapping algorithm. The labels used to define distances, angles, and vectors are described in the text. Arrows indicate the rotation around vectors. The fragments are depicted with different colors that correspond to the different atoms: white, hydrogen; gray, carbon; dark gray (blue), nitrogen; and light gray (red), oxygen. The dashed line represents the formed atomistic backbone bond.
Histogram of (a) A-M3 bond length, (b) A-M2-A angle, and (c) interchain RDF A-A pairs extracted from atomistic (solid line) and CG after reinsertion of atomistic detail (empty circles) at 400 K.
Persistence lengths in the number of backbone bonds obtained from the pseudo-CG and CG simulations at different temperatures. To obtain the value of the in nanometers we consider an averaged value for the CG bond of 3.5 nm.
[(a) and (c)] The time correlation functions, , for HBs between the amide groups at different temperatures for the atomistic and CG simulations calculated from MD trajectories saved every 1 ps (atomistic) and 1.4 ps (CG). [(b) and (d)] Temperature dependence of structure relaxation time plotted as vs for the atomistic and CG simulations. Dash line denotes the fit to an Arrhenius law and solid line denotes the fit to VFT law. In the inset the difference among and is reported for all the simulation temperatures.
(a) Time correlation function calculated from MD trajectories saved every 7 fs for HB between the amide groups at different temperatures in the CG simulations. (b) HB lifetimes obtained from . The solid line represents the linear fit through the points.
(a) Master curve for the chain center-of-mass diffusion coefficient and normalized with respect to their value at 600 K . (b) Behavior of the scaling factor coming from the diffusion coefficient () and from the HB correlation functions .
Static properties for PA-66 obtained from the original atomistic simulations (before coarse graining), the CG simulations, and the atomistic simulation after backmapping. If not specified in parentheses the results are obtained at 400 K.
Structural relaxation times of HBs calculated for atomistic and CG simulations. The last two columns report the time scaling factors calculated from the as well as from the chain center-of-mass diffusion coefficients .
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