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Large protein assemblies, such as virus capsids, may be coarse-grained as aset of rigid domains linked by generalized (rotational and stretching) harmonicsprings. We present a method to obtain the elastic parameters and overdampeddynamics for these springs from all-atom molecular dynamics simulations of onepair of domains at a time. The computed relaxation times of this pair give aconsistency check for the simulation, and (using a fluctuation-dissipationrelationship) we find the corrective force needed to null systematic drifts. Asa first application we predict the stiffness of an HIV capsid layer and therelaxation time for its breathing mode.

Coarse-grained protein-protein stiffnesses and dynamics from all-atom simulations