Chevrot G., Hinsen K. and Kneller G.R.
The Journal of Chemical Physics (2013) 139 (15) 154110 - doi : papers2 ://publication/doi/10.1063/1.4823996
In the present work, we propose a simple model-free approach for the computation of molecular dif- fusion tensors from molecular dynamics trajectories. The method uses a rigid body trajectory of the molecule under consideration, which is constructed a posteriori by an accumulation of quaternion- based superposition fits of consecutive conformations. From the rigid body trajectory, we compute the translational and angular velocities of the molecule and by integration of the latter also the cor- responding angular trajectory. All quantities can be referred to the laboratory frame and a molecule- fixed frame. The 6 × 6 diffusion tensor is computed from the asymptotic slope of the tensorial mean square displacement and, for comparison, also from the Kubo integral of the velocity cor- relation tensor. The method is illustrated for two simple model systems – a water molecule and a lysozyme molecule in bulk water. We give estimations of the statistical accuracy of the calculations.