.. _analysis:

Analysis
========

In this chapter different ways of analyzing your trajectory are
described. The names of the corresponding analysis programs are given.
Specific information on the in- and output of these programs can be
found in the tool documentation :ref:`here <gmx-cmdline>`.
The output files are often
produced as finished Grace/Xmgr graphs.

First, in sec. :ref:`usinggroups`, the group concept in analysis is
explained. :ref:`selections` explains a newer concept of dynamic
selections, which is currently supported by a few tools. Then, the
different analysis tools are presented.

.. toctree::
   :maxdepth: 2

   using-groups
   looking-at-trajectory
   general-properties
   radial-distribution-function
   correlation-function
   curve-fitting
   mean-square-displacement
   bond-angle-dihedral
   radius-of-gyration
   rmsd
   covariance-analysis
   dihedral-pca
   hydrogen-bonds
   protein-related
   interface-related


