Make (most) HTML links to file formats work again

[alexxy/gromacs.git] / src / programs / mdrun / mdrun.cpp

diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp
index 5298cb744d33d08c24debd14b904b64e4536dda9..1462f0f4267a4e073b03339a49d106127ab8b861 100644 (file)
--- a/src/programs/mdrun/mdrun.cpp
+++ b/src/programs/mdrun/mdrun.cpp
@@ -99,14 +99,14 @@ int gmx_mdrun(int argc, char *argv[])
         "should look there for practical advice on using many of the options",
         "available in mdrun.[PAR]",
         "ED (essential dynamics) sampling and/or additional flooding potentials",
-        "are switched on by using the [TT]-ei[tt] flag followed by an [TT].edi[tt]",
-        "file. The [TT].edi[tt] file can be produced with the [TT]make_edi[tt] tool",
+        "are switched on by using the [TT]-ei[tt] flag followed by an [REF].edi[ref]",
+        "file. The [REF].edi[ref] file can be produced with the [TT]make_edi[tt] tool",
         "or by using options in the essdyn menu of the WHAT IF program.",
-        "[TT]mdrun[tt] produces a [TT].xvg[tt] output file that",
+        "[TT]mdrun[tt] produces a [REF].xvg[ref] output file that",
         "contains projections of positions, velocities and forces onto selected",
         "eigenvectors.[PAR]",
         "When user-defined potential functions have been selected in the",
-        "[TT].mdp[tt] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
+        "[REF].mdp[ref] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
         "a formatted table with potential functions. The file is read from",
         "either the current directory or from the [TT]GMXLIB[tt] directory.",
         "A number of pre-formatted tables are presented in the [TT]GMXLIB[tt] dir,",
@@ -122,7 +122,7 @@ int gmx_mdrun(int argc, char *argv[])
         "and finally the table number of the interaction type.[PAR]",
         "The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
         "coordinates and forces when pulling is selected",
-        "in the [TT].mdp[tt] file.[PAR]",
+        "in the [REF].mdp[ref] file.[PAR]",
         "Finally some experimental algorithms can be tested when the",
         "appropriate options have been given. Currently under",
         "investigation are: polarizability.",
@@ -148,7 +148,7 @@ int gmx_mdrun(int argc, char *argv[])
         "A simulation can be continued by reading the full state from file",
         "with option [TT]-cpi[tt]. This option is intelligent in the way that",
         "if no checkpoint file is found, Gromacs just assumes a normal run and",
-        "starts from the first step of the [TT].tpr[tt] file. By default the output",
+        "starts from the first step of the [REF].tpr[ref] file. By default the output",
         "will be appending to the existing output files. The checkpoint file",
         "contains checksums of all output files, such that you will never",
         "loose data when some output files are modified, corrupt or removed.",