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

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

diff --git a/src/tools/gmx_spatial.c b/src/tools/gmx_spatial.c
index a06232308f8a927dc3c94c8fa07fdea20055da57..6053f6f383a35afd9c2a6e052bc1d661b79b9868 100644 (file)
--- a/src/tools/gmx_spatial.c
+++ b/src/tools/gmx_spatial.c
@@ -64,7 +64,7 @@ int gmx_spatial(int argc,char *argv[])
   const char *desc[] = {
     "g_spatial calculates the spatial distribution function and ",
     "outputs it in a form that can be read by VMD as Gaussian98 cube format. ",
-    "This was developed from template.c (gromacs-3.3). ",
+    "This was developed from template.c (GROMACS-3.3). ",
     "For a system of 32K atoms and a 50ns trajectory, the SDF can be generated ",
     "in about 30 minutes, with most of the time dedicated to the two runs through ",
     "trjconv that are required to center everything properly. ",
@@ -81,24 +81,24 @@ int gmx_spatial(int argc,char *argv[])
     "3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans \n",
     "4. run g_spatial on the xtc output of step #3. \n",
     "5. Load grid.cube into VMD and view as an isosurface. \n",
-    "*** Systems such as micelles will require trjconv -pbc cluster between steps 1 and 2\n",
+    "*** Systems such as micelles will require [TT]trjconv -pbc cluster[tt] between steps 1 and 2\n",
     "WARNINGS: \n",
     "The SDF will be generated for a cube that contains all bins that have some non-zero occupancy. ",
-    "However, the preparatory -fit rot+trans option to trjconv implies that your system will be rotating ",
+    "However, the preparatory [TT]-fit rot+trans[tt] option to trjconv implies that your system will be rotating ",
     "and translating in space (in order that the selected group does not). Therefore the values that are ",
     "returned will only be valid for some region around your central group/coordinate that has full overlap ",
     "with system volume throughout the entire translated/rotated system over the course of the trajectory. ",
     "It is up to the user to ensure that this is the case. \n",
     "BUGS: \n",
     "When the allocated memory is not large enough, a segmentation fault may occur. This is usually detected ",
-    "and the program is halted prior to the fault while displaying a warning message suggesting the use of the -nab ",
+    "and the program is halted prior to the fault while displaying a warning message suggesting the use of the [TT]-nab[tt] ",
     "option. However, the program does not detect all such events. If you encounter a segmentation fault, run it again ",
-    "with an increased -nab value. \n",
+    "with an increased [TT]-nab[tt] value. \n",
     "RISKY OPTIONS: \n",
     "To reduce the amount of space and time required, you can output only the coords ",
     "that are going to be used in the first and subsequent run through trjconv. ",
-    "However, be sure to set the -nab option to a sufficiently high value since ",
-    "memory is allocated for cube bins based on the initial coords and the -nab ",
+    "However, be sure to set the [TT]-nab[tt] option to a sufficiently high value since ",
+    "memory is allocated for cube bins based on the initial coords and the [TT]-nab[tt] ",
     "(Number of Additional Bins) option value. \n"
   };