Make (most) HTML links to file formats work again

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_bar.c

diff --git a/src/gromacs/gmxana/gmx_bar.c b/src/gromacs/gmxana/gmx_bar.c
index d6d937152718a51bf7f052af7616eddeebe1fe39..b285678247246c668b29861f6d585fa6af9dc30a 100644 (file)
--- a/src/gromacs/gmxana/gmx_bar.c
+++ b/src/gromacs/gmxana/gmx_bar.c
@@ -3499,13 +3499,13 @@ int gmx_bar(int argc, char *argv[])
 
         "Every individual BAR free energy difference relies on two ",
         "simulations at different states: say state A and state B, as",
-        "controlled by a parameter, [GRK]lambda[grk] (see the [TT].mdp[tt] parameter",
+        "controlled by a parameter, [GRK]lambda[grk] (see the [REF].mdp[ref] parameter",
         "[TT]init_lambda[tt]). The BAR method calculates a ratio of weighted",
         "average of the Hamiltonian difference of state B given state A and",
         "vice versa.",
         "The energy differences to the other state must be calculated",
         "explicitly during the simulation. This can be done with",
-        "the [TT].mdp[tt] option [TT]foreign_lambda[tt].[PAR]",
+        "the [REF].mdp[ref] option [TT]foreign_lambda[tt].[PAR]",
 
         "Input option [TT]-f[tt] expects multiple [TT]dhdl.xvg[tt] files. ",
         "Two types of input files are supported:[BR]",
@@ -3531,14 +3531,14 @@ int gmx_bar(int argc, char *argv[])
         "capitalized letters 'D' and 'H'. The temperature is parsed from ",
         "the legend line containing 'T ='.[PAR]",
 
-        "The input option [TT]-g[tt] expects multiple [TT].edr[tt] files. ",
+        "The input option [TT]-g[tt] expects multiple [REF].edr[ref] files. ",
         "These can contain either lists of energy differences (see the ",
-        "[TT].mdp[tt] option [TT]separate_dhdl_file[tt]), or a series of ",
-        "histograms (see the [TT].mdp[tt] options [TT]dh_hist_size[tt] and ",
+        "[REF].mdp[ref] option [TT]separate_dhdl_file[tt]), or a series of ",
+        "histograms (see the [REF].mdp[ref] options [TT]dh_hist_size[tt] and ",
         "[TT]dh_hist_spacing[tt]).", "The temperature and [GRK]lambda[grk] ",
         "values are automatically deduced from the [TT]ener.edr[tt] file.[PAR]",
 
-        "In addition to the [TT].mdp[tt] option [TT]foreign_lambda[tt], ",
+        "In addition to the [REF].mdp[ref] option [TT]foreign_lambda[tt], ",
         "the energy difference can also be extrapolated from the ",
         "dH/d[GRK]lambda[grk] values. This is done with the[TT]-extp[tt]",
         "option, which assumes that the system's Hamiltonian depends linearly",