Tons of small fixes to documentation.

[alexxy/gromacs.git] / src / tools / gmx_sorient.c

diff --git a/src/tools/gmx_sorient.c b/src/tools/gmx_sorient.c
index 53862d6a80be745d62ab2ef1155837e056f5c554..213eb7f796cea5cd9122a7d766665efc44b9a031 100644 (file)
--- a/src/tools/gmx_sorient.c
+++ b/src/tools/gmx_sorient.c
@@ -127,23 +127,23 @@ int gmx_sorient(int argc,char *argv[])
   const char *desc[] = {
     "[TT]g_sorient[tt] analyzes solvent orientation around solutes.", 
     "It calculates two angles between the vector from one or more",
-    "reference positions to the first atom of each solvent molecule:[BR]",
-    "theta1: the angle with the vector from the first atom of the solvent",
+    "reference positions to the first atom of each solvent molecule:[PAR]",
+    "[GRK]theta[grk]1: the angle with the vector from the first atom of the solvent",
     "molecule to the midpoint between atoms 2 and 3.[BR]",
-    "theta2: the angle with the normal of the solvent plane, defined by the",
-    "same three atoms, or when the option [TT]-v23[tt] is set",
-    "the angle with the vector between atoms 2 and 3.[BR]",
+    "[GRK]theta[grk]2: the angle with the normal of the solvent plane, defined by the",
+    "same three atoms, or, when the option [TT]-v23[tt] is set, ",
+    "the angle with the vector between atoms 2 and 3.[PAR]",
     "The reference can be a set of atoms or",
     "the center of mass of a set of atoms. The group of solvent atoms should",
     "consist of 3 atoms per solvent molecule.",
     "Only solvent molecules between [TT]-rmin[tt] and [TT]-rmax[tt] are",
     "considered for [TT]-o[tt] and [TT]-no[tt] each frame.[PAR]",
-    "[TT]-o[tt]: distribtion of cos(theta1) for rmin<=r<=rmax.[PAR]",
-    "[TT]-no[tt]: distribution of cos(theta2) for rmin<=r<=rmax.[PAR]",
-    "[TT]-ro[tt]: <cos(theta1)> and <3cos^2(theta2)-1> as a function of the",
+    "[TT]-o[tt]: distribtion of cos([GRK]theta[grk]1) for rmin<=r<=rmax.[PAR]",
+    "[TT]-no[tt]: distribution of cos([GRK]theta[grk]2) for rmin<=r<=rmax.[PAR]",
+    "[TT]-ro[tt]: <cos([GRK]theta[grk]1)> and <3cos^2([GRK]theta[grk]2)-1> as a function of the",
     "distance.[PAR]",
     "[TT]-co[tt]: the sum over all solvent molecules within distance r",
-    "of cos(theta1) and 3cos^2(theta2)-1 as a function of r.[PAR]",
+    "of cos([GRK]theta[grk]1) and 3cos^2([GRK]theta[grk]2)-1 as a function of r.[PAR]",
     "[TT]-rc[tt]: the distribution of the solvent molecules as a function of r"
   };