Tons of small fixes to documentation.

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

diff --git a/src/tools/gmx_membed.c b/src/tools/gmx_membed.c
index ddbb528746fe7dff24bab8fc29010517c7f01f96..f9c895642da5d26e2595e606a314fb5830afce49 100644 (file)
--- a/src/tools/gmx_membed.c
+++ b/src/tools/gmx_membed.c
@@ -4283,14 +4283,13 @@ int gmx_membed(int argc,char *argv[])
 {
        const char *desc[] = {
                        "[TT]g_membed[tt] embeds a membrane protein into an equilibrated lipid bilayer at the position",
-                       "and orientation specified by the user.\n",
-                       "\n",
-                       "SHORT MANUAL\n------------\n",
+                       "and orientation specified by the user.[PAR]",
+                       "SHORT MANUAL[BR]------------[BR]",
                        "The user should merge the structure files of the protein and membrane (+solvent), creating a",
                        "single structure file with the protein overlapping the membrane at the desired position and",
-                       "orientation. Box size should be taken from the membrane structure file. The corresponding topology",
+                       "orientation. The box size is taken from the membrane structure file. The corresponding topology",
                        "files should also be merged. Consecutively, create a [TT].tpr[tt] file (input for [TT]g_membed[tt]) from these files,"
-                       "with the following options included in the [TT].mdp[tt] file.\n",
+                       "with the following options included in the [TT].mdp[tt] file.[BR]",
                        " - [TT]integrator      = md[tt][BR]",
                        " - [TT]energygrp       = Protein[tt] (or other group that you want to insert)[BR]",
                        " - [TT]freezegrps      = Protein[tt][BR]",
@@ -4298,32 +4297,29 @@ int gmx_membed(int argc,char *argv[])
                        " - [TT]energygrp_excl  = Protein Protein[tt][BR]",
                        "The output is a structure file containing the protein embedded in the membrane. If a topology",
                        "file is provided, the number of lipid and ",
-                       "solvent molecules will be updated to match the new structure file.\n",
-                       "For a more extensive manual see Wolf et al, J Comp Chem 31 (2010) 2169-2174, Appendix.\n",
-                       "\n",
-                       "SHORT METHOD DESCRIPTION\n",
-                       "------------------------\n",
+                       "solvent molecules will be updated to match the new structure file.[BR]",
+                       "For a more extensive manual see Wolf et al, J Comp Chem 31 (2010) 2169-2174, Appendix.[PAR]",
+                       "SHORT METHOD DESCRIPTION[BR]",
+                       "------------------------[BR]",
                        "1. The protein is resized around its center of mass by a factor [TT]-xy[tt] in the xy-plane",
-                       "(the membrane plane) and a factor [TT]-z[tt] in the z-direction (if the size of the",
+                       "(the membrane plane) and a factor [TT]-z[tt] in the [IT]z[it]-direction (if the size of the",
                        "protein in the z-direction is the same or smaller than the width of the membrane, a",
-                       "[TT]-z[tt] value larger than 1 can prevent that the protein will be enveloped by the lipids).\n",
+                       "[TT]-z[tt] value larger than 1 can prevent that the protein will be enveloped by the lipids).[BR]",
                        "2. All lipid and solvent molecules overlapping with the resized protein are removed. All",
                        "intraprotein interactions are turned off to prevent numerical issues for small values of [TT]-xy[tt]",
-                       " or [TT]-z[tt]\n",
-                       "3. One md step is performed.\n",
+                       " or [TT]-z[tt][BR]",
+                       "3. One md step is performed.[BR]",
                        "4. The resize factor ([TT]-xy[tt] or [TT]-z[tt]) is incremented by a small amount ((1-xy)/nxy or (1-z)/nz) and the",
                        "protein is resized again around its center of mass. The resize factor for the xy-plane",
                        "is incremented first. The resize factor for the z-direction is not changed until the [TT]-xy[tt] factor",
-                       "is 1 (thus after [TT]-nxy[tt] iterations).\n",
-                       "5. Repeat step 3 and 4 until the protein reaches its original size ([TT]-nxy[tt] + [TT]-nz[tt] iterations).\n",
-                       "For a more extensive method description see Wolf et al, J Comp Chem, 31 (2010) 2169-2174.\n",
-                       "\n",
-                       "NOTE\n----\n",
-                       " - Protein can be any molecule you want to insert in the membrane.\n",
+                       "is 1 (thus after [TT]-nxy[tt] iterations).[BR]",
+                       "5. Repeat step 3 and 4 until the protein reaches its original size ([TT]-nxy[tt] + [TT]-nz[tt] iterations).[BR]",
+                       "For a more extensive method description see Wolf et al, J Comp Chem, 31 (2010) 2169-2174.[PAR]",
+                       "NOTE[BR]----[BR]",
+                       " - Protein can be any molecule you want to insert in the membrane.[BR]",
                        " - It is recommended to perform a short equilibration run after the embedding",
                        "(see Wolf et al, J Comp Chem 31 (2010) 2169-2174), to re-equilibrate the membrane. Clearly",
-                       "protein equilibration might require longer.\n",
-                       "\n"
+                       "protein equilibration might require longer.[PAR]"
        };
        t_commrec    *cr;
        t_filenm fnm[] = {