4.4.2 Analysis of backbone trajectories for T4 lysozyme with p-xylene in MD and BLUES While there were no obvious differences for the backbone of the Val111 residue or backbones of residues local to the binding site, there appears to be some larger systemic relaxation that occurs over the course of the longer MD simulation (Figure ). Previous long-timescale simulations (5 µs) of the T4 lysozyme L99A mutant in its apo form capture larger conformational changes as the protein transitions from a ground state to an excited state. During this conformational shift, the binding pocket expands and the χ 1 of phenylalanine 114 relaxes to an alternate rotamer state. Here, in our much shorter microsecond simulation, we may be observing some relaxation towards either the excited or ground states; further analysis is needed to determine if and how the motions we see relate to those previously reported.