No abstract

We study the homogeneous cooling of hard, smooth ellipsoids in three dimensions using event driven numerical simulation. The elongation of the particle has a strong effect on the cooling behavior. Weakly elongated ellipsoids display two distinct cooling regimes. For small times, the translational and rotational energy decay at a different rates. Once their ratio reaches a time-independent value (different from equipartition), the overall temperature of the system decays like t −2 , as predicted by Haff's law. For more elongated ellipsoids the translational and rotational temperatures rapidly reach a constant ratio near unity. The cooling behavior in the homogeneous state can be predicted from Haff's law and the equilibrium collision rate.

Improvements to the confinement method for the calculation of conformational free energy differences are presented. By taking advantage of phase space overlap between simulations at different frequencies, significant gains in accuracy and speed are reached. The optimal frequency spacing for the simulations is obtained from extrapolations of the confinement energy, and relaxation time analysis is used to determine time steps, simulation lengths, and friction coefficients. At postprocessing, interpolation of confinement energies is used to significantly reduce discretization errors in the calculation of conformational free energies. The efficiency of this protocol is illustrated by applications to alanine n-peptides and lactoferricin. For the alanine-n-peptide, errors were reduced between 2- and 10-fold and sampling times between 8- and 67-fold, while for lactoferricin the long sampling times at low frequencies were reduced 10-100-fold.