Protein-related items#
You can also look at the changing of secondary structure elements during your run. For this, you can use the program gmx dssp, which is a native implementation of DSSP algorithm 176.
Analysis of the secondary structure elements of a peptide in time.
One other important analysis of proteins is the so-called Ramachandran plot. This is the projection of the structure on the two dihedral angles \(\phi\) and \(\psi\) of the protein backbone, see Fig. 60:
To evaluate this Ramachandran plot you can use the program gmx rama. A typical output is given in Fig. 61.
When studying \(\alpha\)-helices it is useful to have a helical wheel projection of your peptide, to see whether a peptide is amphipathic. This can be done using the gmx wheel program. Two examples are plotted in Fig. 62.