Dihedral principal component analysis
-------------------------------------
| :ref:`gmx angle `, :ref:`gmx covar `,
:ref:`gmx anaeig `
| Principal component analysis can be performed in dihedral
space \ :ref:`172 ` using |Gromacs|. You start by defining the
dihedral angles of interest in an index file, either using
:ref:`gmx mk_angndx ` or otherwise. Then you use the
:ref:`gmx angle ` program with the ``-or`` flag to
produce a new :ref:`trr` file containing the cosine and sine
of each dihedral angle in two coordinates, respectively. That is, in
the :ref:`trr` file you will have a series of numbers
corresponding to: cos(\ :math:`\phi_1`), sin(\ :math:`\phi_1`),
cos(\ :math:`\phi_2`), sin(\ :math:`\phi_2`), ...,
cos(\ :math:`\phi_n`), sin(\ :math:`\phi_n`), and the array is padded
with zeros, if necessary. Then you can use this :ref:`trr`
file as input for the :ref:`gmx covar ` program and perform
principal component analysis as usual. For this to work you will need
to generate a reference file (:ref:`tpr`,
:ref:`gro`, :ref:`pdb` etc.) containing the same
number of “atoms” as the new :ref:`trr` file, that is for
:math:`n` dihedrals you need 2\ :math:`n`/3 atoms (rounded up if not
an integer number). You should use the ``-nofit`` option
for :ref:`gmx covar ` since the coordinates in the dummy
reference file do not correspond in any way to the information in the
:ref:`trr` file. Analysis of the results is done using
:ref:`gmx anaeig `.