#include <stdlib.h>
#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/matio.h"
-#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxana/cmat.h"
"Option [TT]-prev[tt] produces the comparison with a previous frame",
"the specified number of frames ago.[PAR]",
- "Option [TT]-m[tt] produces a matrix in [TT].xpm[tt] format of",
+ "Option [TT]-m[tt] produces a matrix in [REF].xpm[ref] format of",
"comparison values of each structure in the trajectory with respect to",
"each other structure. This file can be visualized with for instance",
"[TT]xv[tt] and can be converted to postscript with [gmx-xpm2ps].[PAR]",
"Option [TT]-mw[tt] controls whether mass weighting is done or not.",
"If you select the option (default) and ",
- "supply a valid [TT].tpr[tt] file masses will be taken from there, ",
+ "supply a valid [REF].tpr[ref] file masses will be taken from there, ",
"otherwise the masses will be deduced from the [TT]atommass.dat[tt] file in",
"[TT]GMXLIB[tt]. This is fine for proteins, but not",
"necessarily for other molecules. A default mass of 12.011 amu (carbon)",