Make (most) HTML links to file formats work again

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_wham.cpp

diff --git a/src/gromacs/gmxana/gmx_wham.cpp b/src/gromacs/gmxana/gmx_wham.cpp
index b39e99197055bbb63d841fe8097500aaaeef2de9..2e6c0fc27b76fc797136ff9d3baf21017c881092 100644 (file)
--- a/src/gromacs/gmxana/gmx_wham.cpp
+++ b/src/gromacs/gmxana/gmx_wham.cpp
@@ -3132,19 +3132,19 @@ int gmx_wham(int argc, char *argv[])
         "compute a potential of mean force (PMF). [PAR] ",
         "At present, three input modes are supported.[BR]",
         "[TT]*[tt] With option [TT]-it[tt], the user provides a file which contains the",
-        " file names of the umbrella simulation run-input files ([TT].tpr[tt] files),",
+        " file names of the umbrella simulation run-input files ([REF].tpr[ref] files),",
         " AND, with option [TT]-ix[tt], a file which contains file names of",
-        " the pullx [TT]mdrun[tt] output files. The [TT].tpr[tt] and pullx files must",
-        " be in corresponding order, i.e. the first [TT].tpr[tt] created the",
+        " the pullx [TT]mdrun[tt] output files. The [REF].tpr[ref] and pullx files must",
+        " be in corresponding order, i.e. the first [REF].tpr[ref] created the",
         " first pullx, etc.[BR]",
         "[TT]*[tt] Same as the previous input mode, except that the the user",
         " provides the pull force output file names ([TT]pullf.xvg[tt]) with option [TT]-if[tt].",
         " From the pull force the position in the umbrella potential is",
         " computed. This does not work with tabulated umbrella potentials.[BR]"
-        "[TT]*[tt] With option [TT]-ip[tt], the user provides file names of (gzipped) [TT].pdo[tt] files, i.e.",
+        "[TT]*[tt] With option [TT]-ip[tt], the user provides file names of (gzipped) [REF].pdo[ref] files, i.e.",
         " the GROMACS 3.3 umbrella output files. If you have some unusual"
-        " reaction coordinate you may also generate your own [TT].pdo[tt] files and",
-        " feed them with the [TT]-ip[tt] option into to [THISMODULE]. The [TT].pdo[tt] file header",
+        " reaction coordinate you may also generate your own [REF].pdo[ref] files and",
+        " feed them with the [TT]-ip[tt] option into to [THISMODULE]. The [REF].pdo[ref] file header",
         " must be similar to the following:[PAR]",
         "# UMBRELLA      3.0[BR]",
         "# Component selection: 0 0 1[BR]",
@@ -3158,7 +3158,7 @@ int gmx_wham(int argc, char *argv[])
         "may (of course) differ. Following the header, a time column and ",
         "a data column for each pull group follows (i.e. the displacement",
         "with respect to the umbrella center). Up to four pull groups are possible ",
-        "per [TT].pdo[tt] file at present.[PAR]",
+        "per [REF].pdo[ref] file at present.[PAR]",
         "By default, all pull groups found in all pullx/pullf files are used in WHAM. If only ",
         "some of the pull groups should be used, a pull group selection file (option [TT]-is[tt]) can ",
         "be provided. The selection file must contain one line for each tpr file in tpr-files.dat.",
@@ -3174,7 +3174,7 @@ int gmx_wham(int argc, char *argv[])
         "  [TT]-hist[tt]   Histograms output file[BR]",
         "Always check whether the histograms sufficiently overlap.[PAR]",
         "The umbrella potential is assumed to be harmonic and the force constants are ",
-        "read from the [TT].tpr[tt] or [TT].pdo[tt] files. If a non-harmonic umbrella force was applied ",
+        "read from the [REF].tpr[ref] or [REF].pdo[ref] files. If a non-harmonic umbrella force was applied ",
         "a tabulated potential can be provided with [TT]-tab[tt].[PAR]",
         "WHAM OPTIONS[BR]------------[BR]",
         "  [TT]-bins[tt]   Number of bins used in analysis[BR]",
@@ -3213,7 +3213,7 @@ int gmx_wham(int argc, char *argv[])
         "less robust) method such as fitting to a double exponential, you can ",
         "compute the IACTs with [gmx-analyze] and provide them to [THISMODULE] with the file ",
         "[TT]iact-in.dat[tt] (option [TT]-iiact[tt]), which should contain one line per ",
-        "input file ([TT].pdo[tt] or pullx/f file) and one column per pull group in the respective file.[PAR]",
+        "input file ([REF].pdo[ref] or pullx/f file) and one column per pull group in the respective file.[PAR]",
         "ERROR ANALYSIS[BR]--------------[BR]",
         "Statistical errors may be estimated with bootstrap analysis. Use it with care, ",
         "otherwise the statistical error may be substantially underestimated. ",