Convert file format descriptions to rst

[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 b6171209b4b4977951bb251c2456d5fb2e12fae9..d35bf01b99ef031310325ebd739a6e6b7fb42351 100644 (file)
--- a/docs/user-guide/getting-started.rst
+++ b/docs/user-guide/getting-started.rst
@@ -47,7 +47,7 @@ Molecular Topology file (``.top``)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The molecular topology file is generated by the program :ref:`gmx pdb2gmx`.
-:ref:`gmx pdb2gmx` translates a PDB_ structure file of any
+:ref:`gmx pdb2gmx` translates a :ref:`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.
@@ -56,11 +56,11 @@ Molecular Structure file (``.gro``, ``.pdb``)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 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
+also translates the structure file (:ref:`pdb` file) to a GROMOS structure
+file (:ref:`gro` file). The main difference between a :ref:`pdb` file and a gromos
+file is their format and that a :ref:`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
+use a :ref:`PDB` file in all programs. To generate a box of solvent
 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
@@ -73,11 +73,11 @@ topology.
 Molecular Dynamics parameter file (``.mdp``)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The Molecular Dynamics Parameter (mdp_) file contains all information
+The Molecular Dynamics Parameter (:ref:`mdp`) file contains all information
 about the Molecular Dynamics simulation itself e.g. time-step, number
 of steps, temperature, pressure etc. The easiest way of handling such
-a file is by adapting a sample mdp_ file. A `sample mdp file`_ is
-available.
+a file is by adapting a sample :ref:`mdp` file. A :ref:`sample mdp file <mdp>`
+is available.
 
 Index file (``.ndx``)
 ^^^^^^^^^^^^^^^^^^^^^
@@ -90,12 +90,12 @@ not consider the use of index files.
 Run input file (``.tpr``)
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
-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
+The next step is to combine the molecular structure (:ref:`gro` file),
+topology (:ref:`top` file) MD-parameters (:ref:`mdp` file) and (optionally) the
+index file (:ref:`ndx`) to generate a run input file (:ref:`tpr` extension). This
 file contains all information needed to start a simulation with
 |Gromacs|. The :ref:`gmx grompp` program processes all input files and
-generates the run input tpr_ file.
+generates the run input :ref:`tpr` file.
 
 Trajectory file (``.trr``, ``.tng``, or ``.xtc``)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -104,9 +104,9 @@ Once the run input file is available, we can start the simulation. 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).
+file (:ref:`tpr` file). The typical output files of :ref:`gmx mdrun` are the
+trajectory file (:ref:`trr` file), a logfile (:ref:`log` file), and perhaps a
+checkpoint file (:ref:`cpt` file).
 
 Tutorial material
 -----------------