Replace tool HTML help with Sphinx-generated docs

[alexxy/gromacs.git] / docs / user-guide / getting-started.rst

diff --git a/docs/user-guide/getting-started.rst b/docs/user-guide/getting-started.rst
index cbb055e97473e2b16217b9fa04bff17e9743cabb..b6171209b4b4977951bb251c2456d5fb2e12fae9 100644 (file)
--- a/docs/user-guide/getting-started.rst
+++ b/docs/user-guide/getting-started.rst
@@ -46,8 +46,8 @@ encounter.
 Molecular Topology file (``.top``)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The molecular topology file is generated by the program `gmx
-pdb2gmx`_. `gmx pdb2gmx`_ translates a PDB_ structure file of any
+The molecular topology file is generated by the program :ref:`gmx pdb2gmx`.
+:ref:`gmx pdb2gmx` translates a PDB_ structure file of any
 peptide or protein to a molecular topology file. This topology file
 contains a complete description of all the interactions in your
 peptide or protein.
@@ -55,19 +55,19 @@ peptide or protein.
 Molecular Structure file (``.gro``, ``.pdb``)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-When `gmx pdb2gmx`_ is executed to generate a molecular topology, it
+When :ref:`gmx pdb2gmx` is executed to generate a molecular topology, it
 also translates the structure file (pdb_ file) to a GROMOS structure
 file (gro_ file). The main difference between a pdb_ file and a gromos
 file is their format and that a gro_ file can also hold
 velocities. However, if you do not need the velocities, you can also
 use a PDB_ file in all programs. To generate a box of solvent
-molecules around the peptide, the program `gmx solvate`_ is
-used. First the program `gmx editconf`_ should be used to define a box
-of appropriate size around the molecule. `gmx solvate`_ solvates a
+molecules around the peptide, the program :ref:`gmx solvate` is
+used. First the program :ref:`gmx editconf` should be used to define a box
+of appropriate size around the molecule. :ref:`gmx solvate` solvates a
 solute molecule (the peptide) into any solvent (in this case,
-water). The output of `gmx solvate`_ is a gromos structure file of the
-peptide solvated in water. `gmx solvate`_ also changes the molecular
-topology file (generated by `gmx pdb2gmx`_) to add solvent to the
+water). The output of :ref:`gmx solvate` is a gromos structure file of the
+peptide solvated in water. :ref:`gmx solvate` also changes the molecular
+topology file (generated by :ref:`gmx pdb2gmx`) to add solvent to the
 topology.
 
 Molecular Dynamics parameter file (``.mdp``)
@@ -94,17 +94,17 @@ The next step is to combine the molecular structure (gro_ file),
 topology (top_ file) MD-parameters (mdp_ file) and (optionally) the
 index file (ndx_) to generate a run input file (tpr_ extension). This
 file contains all information needed to start a simulation with
-|Gromacs|. The `gmx grompp`_ program processes all input files and
+|Gromacs|. The :ref:`gmx grompp` program processes all input files and
 generates the run input tpr_ file.
 
 Trajectory file (``.trr``, ``.tng``, or ``.xtc``)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Once the run input file is available, we can start the simulation. The
-program which starts the simulation is called `gmx mdrun`_ (or
-sometimes just mdrun, or mdrun_mpi). The only input file of `gmx
-mdrun`_ that you usually need in order to start a run is the run input
-file (tpr_ file). The typical output files of `gmx mdrun`_ are the
+program which starts the simulation is called :ref:`gmx mdrun` (or
+sometimes just mdrun, or mdrun_mpi). The only input file of :ref:`gmx mdrun`
+that you usually need in order to start a run is the run input
+file (tpr_ file). The typical output files of :ref:`gmx mdrun` are the
 trajectory file (trr_ file), a logfile (log_ file), and perhaps a
 checkpoint file (cpt_ file).