Lots of editorial fixes to descriptions, etc. to make the manual

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

diff --git a/src/tools/gmx_membed.c b/src/tools/gmx_membed.c
index 2b573bdb98b5733bc973ab59cda8b77326733fa0..ddbb528746fe7dff24bab8fc29010517c7f01f96 100644 (file)
--- a/src/tools/gmx_membed.c
+++ b/src/tools/gmx_membed.c
@@ -4303,25 +4303,25 @@ int gmx_membed(int argc,char *argv[])
                        "\n",
                        "SHORT METHOD DESCRIPTION\n",
                        "------------------------\n",
-                       "1. The protein is resized around its center of mass by a factor -xy in the xy-plane",
-                       "(the membrane plane) and a factor -z in the z-direction (if the size of the",
+                       "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",
                        "protein in the z-direction is the same or smaller than the width of the membrane, a",
-                       "-z 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).\n",
                        "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 -xy",
-                       " or -z\n",
+                       "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",
-                       "4. The resize factor (-xy or -z) is incremented by a small amount ((1-xy)/nxy or (1-z)/nz) and the",
+                       "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 -xy factor",
-                       "is 1 (thus after -nxy iteration).\n",
-                       "5. Repeat step 3 and 4 until the protein reaches its original size (-nxy + -nz iterations).\n",
-                       "For a more extensive method descrition see Wolf et al, J Comp Chem, 31 (2010) 2169-2174.\n",
+                       "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",
                        " - 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",
+                       "(see Wolf et al, J Comp Chem 31 (2010) 2169-2174), to re-equilibrate the membrane. Clearly",
                        "protein equilibration might require longer.\n",
                        "\n"
        };