The observation of cosine-like appearance of the principal mode projections indicates that, as in the case of the Argon gas, the protein motion is primarily diffusive. What does that mean? That most likely means that the protein is exploring a rather flat energy landscape, as a multidimensional random walk, without observing any major barriers. This is a strong indication that the trajectory has not converged, i.e. has not reached equilibrium. The "cosine content" can be obtained from "g_analyze -cc", yielding a powerful convergence criterion. Note that the fact that a high cosine content in a principal mode from a protein trajectory does not mean that the direction corresponding to that mode is not meaningful, it just means that the motion has not yet converged. Whether a direction is meaningful or not can be analyzed by checking how similar the principal modes from one part of the trajectory are to those obtained from another part. Such a comparison can be carried out using the overlap measure activated by "g_anaeig -over".