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1 .. _analysis:
3 Analysis
4 ========
6 In this chapter different ways of analyzing your trajectory are
7 described. The names of the corresponding analysis programs are given.
8 Specific information on the in- and output of these programs can be
9 found in the tool documentation :ref:`here <gmx-cmdline>`.
10 The output files are often
11 produced as finished Grace/Xmgr graphs.
13 First, in sec. :ref:`usinggroups`, the group concept in analysis is
14 explained. :ref:`selections` explains a newer concept of dynamic
15 selections, which is currently supported by a few tools. Then, the
16 different analysis tools are presented.
18 .. toctree::
19    :maxdepth: 2
21    analysis/using-groups
22    analysis/looking-at-trajectory
23    analysis/general-properties
24    analysis/radial-distribution-function
25    analysis/correlation-function
26    analysis/curve-fitting
27    analysis/mean-square-displacement
28    analysis/bond-angle-dihedral
29    analysis/radius-of-gyration
30    analysis/rmsd
31    analysis/covariance-analysis
32    analysis/dihedral-pca
33    analysis/hydrogen-bonds
34    analysis/protein-related
35    analysis/interface-related