The molecular dynamics of dipeptides of natural amino acids were examined using protocols that do not violate the principle of equal distribution of energy over the degrees of freedom. Comparative analysis involved autocorrelation functions of complex exponentials from dihedrals. The mutual influence of residues was classified by the effects on the dynamic properties of the neighbors.

We use molecular dynamics simulation to examine the conformational possibilities in solution for the peptide MEHFPGP (Semax) representing the minimal nootropic fragment of MSH, and its versions with N-terminal substitutions of K, G, or R for M. We discuss the possible relationship between molecule structure and physiological activity, considering the influence of Coulomb interactions on the dynamics and the putative stabilization of a certain peptide conformation at pH < 6.