{
const char *desc[] = {
"tpbconv can edit run input files in four ways.[PAR]",
- "[BB]1st.[bb] by modifying the number of steps in a run input file",
+ "[BB]1.[bb] by modifying the number of steps in a run input file",
"with options [TT]-extend[tt], [TT]-until[tt] or [TT]-nsteps[tt]",
"(nsteps=-1 means unlimited number of steps)[PAR]",
- "[BB]2nd.[bb] (OBSOLETE) by creating a run input file",
+ "[BB]2.[bb] (OBSOLETE) by creating a run input file",
"for a continuation run when your simulation has crashed due to e.g.",
"a full disk, or by making a continuation run input file.",
"This option is obsolete, since mdrun now writes and reads",
"checkpoint files.",
- "Note that a frame with coordinates and velocities is needed.",
+ "[BB]Note[bb] that a frame with coordinates and velocities is needed.",
"When pressure and/or Nose-Hoover temperature coupling is used",
"an energy file can be supplied to get an exact continuation",
"of the original run.[PAR]",
- "[BB]3rd.[bb] by creating a tpx file for a subset of your original",
+ "[BB]3.[bb] by creating a tpx file for a subset of your original",
"tpx file, which is useful when you want to remove the solvent from",
"your tpx file, or when you want to make e.g. a pure Ca tpx file.",
- "Note that you may need to use -nsteps -1 (or similar) to get",
+ "Note that you may need to use [TT]-nsteps -1[tt] (or similar) to get",
"this to work.",
"[BB]WARNING: this tpx file is not fully functional[bb].[PAR]",
- "[BB]4th.[bb] by setting the charges of a specified group",
+ "[BB]4.[bb] by setting the charges of a specified group",
"to zero. This is useful when doing free energy estimates",
"using the LIE (Linear Interaction Energy) method."
};