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.. _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
|
