Protein-related items --------------------- | :ref:`gmx do_dssp `, :ref:`gmx rama `, :ref:`gmx wheel ` | To analyze structural changes of a protein, you can calculate the radius of gyration or the minimum residue distances over time (see sec. :ref:`rg`), or calculate the RMSD (sec. :ref:`rmsd`). You can also look at the changing of *secondary structure elements* during your run. For this, you can use the program :ref:`gmx do_dssp `, which is an interface for the commercial program ``DSSP``  :ref:`176 `. For further information, see the ``DSSP`` manual. A typical output plot of :ref:`gmx do_dssp ` is given in :numref:`Fig. %s `. .. _fig-dssp:  .. figure:: plots/dssp.* :width: 12.00000cm 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 :math:`\phi` and :math:`\psi` of the protein backbone, see :numref:`Fig. %s `:  .. _fig-phipsi: .. figure:: plots/phipsi.* :width: 8.00000cm Definition of the dihedral angles :math:`\phi` and :math:`\psi` of the protein backbone. To evaluate this Ramachandran plot you can use the program :ref:`gmx rama `. A typical output is given in :numref:`Fig. %s `. .. _fig-rama: .. figure:: plots/rama.*  :width: 15.00000cm Ramachandran plot of a small protein. When studying :math:`\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 :ref:`gmx wheel ` program. Two examples are plotted in :numref:`Fig. %s `. .. _fig-hprwheel: .. figure:: plots/hpr-wheel.* :width: 10.00000cm Helical wheel projection of the N-terminal helix of HPr.