Replace some [BR] in help texts with rst literals

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

diff --git a/src/gromacs/gmxana/gmx_energy.c b/src/gromacs/gmxana/gmx_energy.c
index e5c51fd950dc49217fb18150908b3f3d6eeccd1b..89db7f316e087c8d76bd94d86c55b77cd36485d5 100644 (file)
--- a/src/gromacs/gmxana/gmx_energy.c
+++ b/src/gromacs/gmxana/gmx_energy.c
@@ -1915,21 +1915,27 @@ int gmx_energy(int argc, char *argv[])
         "from the [TT]ener.edr[tt] file.[PAR]",
 
         "With [TT]-fee[tt] an estimate is calculated for the free-energy",
-        "difference with an ideal gas state: [BR]",
-        "  [GRK]Delta[grk] A = A(N,V,T) - A[SUB]idealgas[sub](N,V,T) = kT [LN][CHEVRON][EXP]U[SUB]pot[sub]/kT[exp][chevron][ln][BR]",
-        "  [GRK]Delta[grk] G = G(N,p,T) - G[SUB]idealgas[sub](N,p,T) = kT [LN][CHEVRON][EXP]U[SUB]pot[sub]/kT[exp][chevron][ln][BR]",
+        "difference with an ideal gas state::",
+        "",
+        "  [GRK]Delta[grk] A = A(N,V,T) - A[SUB]idealgas[sub](N,V,T) = kT [LN][CHEVRON][EXP]U[SUB]pot[sub]/kT[exp][chevron][ln]",
+        "  [GRK]Delta[grk] G = G(N,p,T) - G[SUB]idealgas[sub](N,p,T) = kT [LN][CHEVRON][EXP]U[SUB]pot[sub]/kT[exp][chevron][ln]",
+        "",
         "where k is Boltzmann's constant, T is set by [TT]-fetemp[tt] and",
         "the average is over the ensemble (or time in a trajectory).",
         "Note that this is in principle",
         "only correct when averaging over the whole (Boltzmann) ensemble",
         "and using the potential energy. This also allows for an entropy",
-        "estimate using:[BR]",
-        "  [GRK]Delta[grk] S(N,V,T) = S(N,V,T) - S[SUB]idealgas[sub](N,V,T) = ([CHEVRON]U[SUB]pot[sub][chevron] - [GRK]Delta[grk] A)/T[BR]",
+        "estimate using::",
+        "",
+        "  [GRK]Delta[grk] S(N,V,T) = S(N,V,T) - S[SUB]idealgas[sub](N,V,T) = ([CHEVRON]U[SUB]pot[sub][chevron] - [GRK]Delta[grk] A)/T",
         "  [GRK]Delta[grk] S(N,p,T) = S(N,p,T) - S[SUB]idealgas[sub](N,p,T) = ([CHEVRON]U[SUB]pot[sub][chevron] + pV - [GRK]Delta[grk] G)/T",
-        "[PAR]",
+        "",
 
         "When a second energy file is specified ([TT]-f2[tt]), a free energy",
-        "difference is calculated [BR] dF = -kT [LN][CHEVRON][EXP]-(E[SUB]B[sub]-E[SUB]A[sub])/kT[exp][chevron][SUB]A[sub][ln] ,",
+        "difference is calculated::",
+        "",
+        "  dF = -kT [LN][CHEVRON][EXP]-(E[SUB]B[sub]-E[SUB]A[sub])/kT[exp][chevron][SUB]A[sub][ln] ,",
+        "",
         "where E[SUB]A[sub] and E[SUB]B[sub] are the energies from the first and second energy",
         "files, and the average is over the ensemble A. The running average",
         "of the free energy difference is printed to a file specified by [TT]-ravg[tt].",