  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.
