Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Coarse-grained protein-protein stiffnesses and dynamics from all-atom
  simulations   Large protein assemblies, such as virus capsids, may be coarse-grained as a
set of rigid domains linked by generalized (rotational and stretching) harmonic
springs. We present a method to obtain the elastic parameters and overdamped
dynamics for these springs from all-atom molecular dynamics simulations of one
pair of domains at a time. The computed relaxation times of this pair give a
consistency check for the simulation, and (using a fluctuation-dissipation
relationship) we find the corrective force needed to null systematic drifts. As
a first application we predict the stiffness of an HIV capsid layer and the
relaxation time for its breathing mode.

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The categories of this paper are: eess
11
The categories of this paper are: hep-lat
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The categories of this paper are: acc-phys
1
The categories of this paper are: cs
3
The categories of this paper are: physics
0
The categories of this paper are: hep-ph
12
The categories of this paper are: nucl-th
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The categories of this paper are: solv-int
36
The categories of this paper are: cmp-lg
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The categories of this paper are: supr-con
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The categories of this paper are: dg-ga
13
The categories of this paper are: quant-ph
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The categories of this paper are: plasm-ph
9
The categories of this paper are: nlin
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The categories of this paper are: econ
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The categories of this paper are: stat