  We describe a novel coarse-grained simulation method for modelling the
dynamics of globular macromolecules, such as proteins. The macromolecule is
treated as a continuum that is subject to thermal fluctuations. The model
includes a non-linear treatment of elasticity and viscosity with thermal noise
that is solved using finite element analysis. We have validated the method by
demonstrating that the model provides average kinetic and potential energies
that are in agreement with the classical equipartition theorem. In addition, we
have performed Fourier analysis on the simulation trajectories obtained for a
series of linear beams to confirm that the correct average energies are present
in the first two Fourier bending modes. We have then used the new modelling
method to simulate the thermal fluctuations of a representative protein over
500ns timescales. Using reasonable parameters for the material properties, we
have demonstrated that the overall deformation of the biomolecule is consistent
with the results obtained for proteins in general from atomistic molecular
dynamics simulations.
