Tons of tiny changes to documentation. Manual looks prettier now.

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

diff --git a/src/tools/gmx_genbox.c b/src/tools/gmx_genbox.c
index 33d98b90b14082f6a268ce9fb971c0ed6a092428..691816c069066ad23a459356dc847ec83ecd5d3f 100644 (file)
--- a/src/tools/gmx_genbox.c
+++ b/src/tools/gmx_genbox.c
@@ -600,12 +600,12 @@ static void update_top(t_atoms *atoms,matrix box,int NFILE,t_filenm fnm[],
 int gmx_genbox(int argc,char *argv[])
 {
   const char *desc[] = {
-    "Genbox can do one of 3 things:[PAR]",
+    "genbox can do one of 3 things:[PAR]",
     
-    "1) Generate a box of solvent. Specify -cs and -box. Or specify -cs and",
-    "-cp with a structure file with a box, but without atoms.[PAR]",
+    "1) Generate a box of solvent. Specify [TT]-cs[tt] and [TT]-box[tt]. Or specify [TT]-cs[tt] and",
+    "[TT]-cp[tt] with a structure file with a box, but without atoms.[PAR]",
     
-    "2) Solvate a solute configuration, eg. a protein, in a bath of solvent ",
+    "2) Solvate a solute configuration, e.g. a protein, in a bath of solvent ",
     "molecules. Specify [TT]-cp[tt] (solute) and [TT]-cs[tt] (solvent). ",
     "The box specified in the solute coordinate file ([TT]-cp[tt]) is used,",
     "unless [TT]-box[tt] is set.",
@@ -614,9 +614,9 @@ int gmx_genbox(int argc,char *argv[])
     "to change the box dimensions and center the solute.",
     "Solvent molecules are removed from the box where the ",
     "distance between any atom of the solute molecule(s) and any atom of ",
-    "the solvent molecule is less than the sum of the VanderWaals radii of ",
-    "both atoms. A database ([TT]vdwradii.dat[tt]) of VanderWaals radii is ",
-    "read by the program, atoms not in the database are ",
+    "the solvent molecule is less than the sum of the van der Waals radii of ",
+    "both atoms. A database ([TT]vdwradii.dat[tt]) of van der Waals radii is ",
+    "read by the program, and atoms not in the database are ",
     "assigned a default distance [TT]-vdwd[tt].",
     "Note that this option will also influence the distances between",
     "solvent molecules if they contain atoms that are not in the database.",
@@ -626,11 +626,11 @@ int gmx_genbox(int argc,char *argv[])
     "at random positions.",
     "The program iterates until [TT]nmol[tt] molecules",
     "have been inserted in the box. To test whether an insertion is ",
-    "successful the same VanderWaals criterium is used as for removal of ",
+    "successful the same van der Waals criterium is used as for removal of ",
     "solvent molecules. When no appropriately ",
     "sized holes (holes that can hold an extra molecule) are available the ",
     "program tries for [TT]-nmol[tt] * [TT]-try[tt] times before giving up. ",
-    "Increase -try if you have several small holes to fill.[PAR]",
+    "Increase [TT]-try[tt] if you have several small holes to fill.[PAR]",
     
     "The default solvent is Simple Point Charge water (SPC), with coordinates ",
     "from [TT]$GMXLIB/spc216.gro[tt]. These coordinates can also be used",
@@ -654,11 +654,11 @@ int gmx_genbox(int argc,char *argv[])
     "longest molecule axis along a box edge. This way the amount of solvent",
     "molecules necessary is reduced.",
     "It should be kept in mind that this only works for",
-    "short simulations, as eg. an alpha-helical peptide in solution can ",
+    "short simulations, as e.g. an alpha-helical peptide in solution can ",
     "rotate over 90 degrees, within 500 ps. In general it is therefore ",
     "better to make a more or less cubic box.[PAR]",
     
-    "Setting -shell larger than zero will place a layer of water of",
+    "Setting [TT]-shell[tt] larger than zero will place a layer of water of",
     "the specified thickness (nm) around the solute. Hint: it is a good",
     "idea to put the protein in the center of a box first (using editconf).",
     "[PAR]",