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Rigorous coarse-graining for the dynamics of linear systems with applications to relaxation dynamics in proteins
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10.1063/1.3613678
/content/aip/journal/jcp/135/5/10.1063/1.3613678
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/5/10.1063/1.3613678

Figures

Image of FIG. 1.
FIG. 1.

A case study of coarse-graining: relaxation modes in a toy model of a linear triatomic molecule. (a) The toy model consists of three beads connected by springs and immersed in viscous solvent. The displacement of the middle bead is treated as the “slave” degree of freedom that is to be eliminated by coarse-graining. (b) Errors in the estimate of the slowest relaxation rate for various approximation orders. (c) Correlation coefficient between the exact relaxation eigenmode and that predicted by the coarse-grained model, at different levels of approximation.

Image of FIG. 2.
FIG. 2.

Structure of the trp-cage (pdb code 1L2Y). One-bead-per-residue coarse-grained model employed the positions of the α-carbons (blue) as the master degrees of freedom. In addition to the α-carbon, two-bead-per-residue model employed a second carbon to represent the configuration of each amino acid residue except for glycine: This second carbon was chosen to be either the β-carbon (red) or the side-chain carbon separated from the corresponding α-carbon by the maximum number of bonds (green).

Image of FIG. 3.
FIG. 3.

One-bead-per-residue model of trp-cage: Errors in the slowest relaxation rates computed for various approximation orders. Here, “e (0m)” refers to the modified zeroth order model with rescaled friction coefficients. See text for further details.

Image of FIG. 4.
FIG. 4.

One-bead-per-residue model of trp-cage: Correlation coefficients between the exact and approximate relaxation eigenmodes at various approximation orders.

Image of FIG. 5.
FIG. 5.

Two-beads-per-residue model of trp-cage: Correlation coefficients between the exact and approximate relaxation eigenmodes at various approximation orders.

Tables

Generic image for table
Table I.

Number of relaxation modes accurately captured by various orders of approximation of the one- and two-bead-per-residue coarse-grained models. “Accurately” in this case is defined as having a correlation coefficient greater than 0.75.

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/content/aip/journal/jcp/135/5/10.1063/1.3613678
2011-08-04
2014-04-17
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Rigorous coarse-graining for the dynamics of linear systems with applications to relaxation dynamics in proteins
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/5/10.1063/1.3613678
10.1063/1.3613678
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