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