Fix some broken links in HTML pages

Links to programs need to be prefixed with the relative path, as well as
"gmx-".  Also added the "gmx " prefix to the displayed names.

Change-Id: I60bd0a58761a725804aa4c5b02619c3031ae7d26

diff --git a/share/html/online/flow.html b/share/html/online/flow.html
index 655fc5973a0d9411240c5a6e314d345ecb8a004a..95ef4ae5d32dac34533842c3cfb532d32acb31a2 100644 (file)
--- a/share/html/online/flow.html
+++ b/share/html/online/flow.html
@@ -21,7 +21,7 @@ these consist of cycles: grompp -> mdrun.
 <TR>
 <TD COLSPAN=2 ALIGN=LEFT>Generate a GROMACS topology </TD>
 <TD></TD>
-<TD BGCOLOR=#777777 COLSPAN=3 ALIGN=CENTER>&nbsp;<A HREF=pdb2gmx.html onMouseOver="window.status='Convert PDB file to GROMAX coordinate file and topology'; return true"><B>pdb2gmx</B></A>&nbsp;</TD>
+<TD BGCOLOR=#777777 COLSPAN=3 ALIGN=CENTER>&nbsp;<A HREF=../programs/gmx-pdb2gmx.html onMouseOver="window.status='Convert PDB file to GROMAX coordinate file and topology'; return true"><B>gmx pdb2gmx</B></A>&nbsp;</TD>
 <TD><IMG SRC=../images/flow_vrule.gif></TD>
 </TR>
 
@@ -56,7 +56,7 @@ these consist of cycles: grompp -&gt; mdrun.
 <TR>
 <TD COLSPAN=2 ALIGN=left>Enlarge the box</TD>
 <TD></TD>
-<TD ALIGN=CENTER BGCOLOR=#777777>&nbsp;&nbsp;<A HREF=editconf.html onMouseOver="window.status='Adjust boxsize and placement of molecule'; return true"><B>editconf</B></A>&nbsp;&nbsp;</TD>
+<TD ALIGN=CENTER BGCOLOR=#777777>&nbsp;&nbsp;<A HREF=../programs/gmx-editconf.html onMouseOver="window.status='Adjust boxsize and placement of molecule'; return true"><B>gmx editconf</B></A>&nbsp;&nbsp;</TD>
 <TD></TD>
 <TD><IMG SRC=../images/flow_vrule.gif></TD>
 </TR>
@@ -89,7 +89,7 @@ these consist of cycles: grompp -&gt; mdrun.
 <TR>
 <TD COLSPAN=2 ALIGN=LEFT>Solvate protein</TD>
 <TD></TD>
-<TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777>&nbsp;<A HREF=../programs/gmx-solvate.html onMouseOver="window.status='Fill box with water (solvate molecule)'; return true"><B>solvate</B></A>&nbsp;</TD>
+<TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777>&nbsp;<A HREF=../programs/gmx-solvate.html onMouseOver="window.status='Fill box with water (solvate molecule)'; return true"><B>gmx solvate</B></A>&nbsp;</TD>
 <TD><IMG SRC=../images/flow_vrule.gif></TD>
 </TR>
 
@@ -124,7 +124,7 @@ these consist of cycles: grompp -&gt; mdrun.
 <TR>
 <TD COLSPAN=2 ALIGN=LEFT>Generate mdrun input file</TD>
 <TD></TD>
-<TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777>&nbsp; <A HREF=grompp.html onMouseOver="window.status='Process parameters, coordinates and topology and write binary topology'; return true"><B>grompp</B></A> &nbsp;</TD>
+<TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777>&nbsp; <A HREF=../programs/gmx-grompp.html onMouseOver="window.status='Process parameters, coordinates and topology and write binary topology'; return true"><B>gmx grompp</B></A> &nbsp;</TD>
 <TD><IMG SRC=../images/flow_vrule.gif></TD>
 <TD></TD>
 <TD></TD>
@@ -162,7 +162,7 @@ these consist of cycles: grompp -&gt; mdrun.
 <TR>
 <TD COLSPAN=2>Run the simulation (EM or MD)</TD>
 <TD></TD>
-<TD  COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777>&nbsp;<A HREF=mdrun.html onMouseOver="window.status='The moment you have all been waiting for! START YOUR MD RUN'; return true"><B>mdrun</B></A>&nbsp;</TD>
+<TD  COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777>&nbsp;<A HREF=../programs/gmx-mdrun.html onMouseOver="window.status='The moment you have all been waiting for! START YOUR MD RUN'; return true"><B>gmx mdrun</B></A>&nbsp;</TD>
 <TD></TD>
 </TR>
 
@@ -197,9 +197,9 @@ these consist of cycles: grompp -&gt; mdrun.
 <TR>
 <TD COLSPAN=2 ALIGN=LEFT>Analysis</TD>
 <TD></TD>
-<TD ALIGN=CENTER BGCOLOR=#777777>&nbsp;&nbsp;<A HREF=../online.html onMouseOver="window.status='Your favourite GROMACS analysis tool'; return true"><B>g_...</B></A>&nbsp;&nbsp;<BR>&nbsp;&nbsp;<A HREF=ngmx.html onMouseOver="window.status='ngmx, the GROMACS trajectory viewer'; return true"><B>ngmx</B></A>&nbsp;&nbsp;</TD>
+<TD ALIGN=CENTER BGCOLOR=#777777>&nbsp;&nbsp;<A HREF=../online.html onMouseOver="window.status='Your favourite GROMACS analysis tool'; return true"><B>g_...</B></A>&nbsp;&nbsp;<BR>&nbsp;&nbsp;<A HREF=../programs/gmx-view.html onMouseOver="window.status='gmx view, the GROMACS trajectory viewer'; return true"><B>gmx view</B></A>&nbsp;&nbsp;</TD>
 <TD></TD>
-<TD ALIGN=CENTER BGCOLOR=#777777>&nbsp;&nbsp;<A HREF=g_energy.html onMouseOver="window.status='Energy plots, averages and  fluctuations'; return true"><B>g_energy</B></A>&nbsp;&nbsp;</TD>
+<TD ALIGN=CENTER BGCOLOR=#777777>&nbsp;&nbsp;<A HREF=../programs/gmx-energy.html onMouseOver="window.status='Energy plots, averages and  fluctuations'; return true"><B>gmx energy</B></A>&nbsp;&nbsp;</TD>
 <TD><IMG SRC=../images/flow_vrule.gif></TD>
 </TR>
 

diff --git a/share/html/online/getting_started.html b/share/html/online/getting_started.html
index b695a06d33a2ed483ed189b96fa24f1cbcd45338..d9de09fad5adeccebd88ba6de4ab6e03255378d8 100644 (file)
--- a/share/html/online/getting_started.html
+++ b/share/html/online/getting_started.html
@@ -125,16 +125,18 @@ encounter during the tutorial.
 <h3><A NAME="top">Molecular Topology file (<TT><a href="top.html">.top</a></TT>)</A></h3>
 <DD>
 The molecular topology file is generated by the program <TT>
-<a href="pdb2gmx.html">pdb2gmx</a></TT>. <a href="pdb2gmx.html">pdb2gmx</a> translates a <a href="pdb.html">pdb</a> structure file of any peptide
-or protein
+<a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a></TT>.
+<a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a> translates a
+<a href="pdb.html">pdb</a> 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.
 <P></P>
-       
+
 <DT>
 <h3><A NAME="gro">Molecular Structure file (<TT><a href="gro.html">.gro</a></TT>, <TT><a href="pdb.html">.pdb</a></TT>)</A></h3>
 <DD>
-When the <a href="pdb2gmx.html">pdb2gmx</a> program is executed to generate a molecular
+When the <a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a> program is executed
+to generate a molecular
 topology, it also translates the structure file (<TT><a href="pdb.html">.pdb</a></TT> file) 
 to a gromos
 structure file (<TT><a href="gro.html">.gro</a></TT> file). The main difference between a 
@@ -143,15 +145,16 @@ a <TT><a href="gro.html">.gro</a></TT> file can also hold velocities. However, i
 velocities, you can also use a <a href="pdb.html">pdb</a> file in all programs.
 To generate a box of solvent molecules
 around the peptide, the program 
-<a href="solvate.html">gmx solvate</a> is used. First the program
-<a href="editconf.html">editconf</a> should be used to
+<a href="../programs/gmx-solvate.html">gmx solvate</a> is used. First the program
+<a href="../programs/gmx-editconf.html">gmx editconf</a> should be used to
 define a box of appropriate size around the molecule.
-<a href="solvate.html">gmx solvate</a>
+<a href="../programs/gmx-solvate.html">gmx solvate</a>
 solvates a solute molecule (the peptide) into any solvent (in this
-case water). The output of <TT><a href="solvate.html">gmx solvate</a></TT> is a gromos structure file of
-the peptide solvated in water. The <a href="solvate.html">gmx solvate</a> program also changes the
-molecular topology file (generated by <a href="pdb2gmx.html">pdb2gmx</a>) to add solvent
-to the topology. 
+case water). The output of <TT><a href="../programs/gmx-solvate.html">gmx solvate</a></TT>
+is a gromos structure file of the peptide solvated in water. The
+<a href="../programs/gmx-solvate.html">gmx solvate</a> program also changes the
+molecular topology file (generated by <a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a>)
+to add solvent to the topology.
 <P></P>
 
 <DT>
@@ -182,9 +185,10 @@ topology (<TT><a href="top.html">.top</a></TT> file) MD-parameters (<TT><a href=
 (optionally) the
 index file (<TT><a href="ndx.html">ndx</a></TT>) to generate a run input file (<TT><a href="tpr.html">.tpr</a></tt> extension or
 <TT><a href="tpb.html">.tpb</a></tt> if you don't have XDR).
-This file contains all information needed to start a simulation with GROMACS. 
-The <a href="grompp.html">
-grompp</a> program processes all input files and generates the run input
+This file contains all information needed to start a simulation with GROMACS.
+The
+<a href="../programs/gmx-grompp.html">gmx grompp</a> program processes all
+input files and generates the run input
 <tt><a href="tpr.html">.tpr</a></tt> file.
 <P></P>
 
@@ -193,11 +197,12 @@ grompp</a> program processes all input files and generates the run input
 <DD>
 Once the run input file is available, we can start the
 simulation. The program which starts the simulation is called 
-<a href="mdrun.html">mdrun</a>. The only input file
-of <TT><a href="mdrun.html">mdrun</a></TT> you usually need to start a run 
+<a href="../programs/gmx-mdrun.html">gmx mdrun</a>. The only input file
+of <TT><a href="../programs/gmx-mdrun.html">gmx mdrun</a></TT> you usually need
+to start a run
 is the run input file (<TT><a href="tpr.html">.tpr</a></TT> file).
 The output files of 
-<TT><a href="mdrun.html">mdrun</a></TT> are the
+<TT><a href="../programs/gmx-mdrun.html">gmx mdrun</a></TT> are the
 trajectory file (<TT><a href="trr.html">.trr</a></TT> file
 or <TT><a href="trj.html">.trj</a></TT> if you don't have XDR) and a logfile (
 <TT><a href="log.html">.log</A></TT> file).