docs/reference-manual/analysis.rst

   1 .. _analysis:
   2
   3 Analysis
   4 ========
   5
   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.
  12
  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.
  17
  18 .. toctree::
  19    :maxdepth: 2
  20
  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
  36
  37