Move read_tps_conf() to confio.h

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_msd.c

diff --git a/src/gromacs/gmxana/gmx_msd.c b/src/gromacs/gmxana/gmx_msd.c
index 6913929759c83a52aaf579d3c62049646d2cfb85..3a6361d8969d93c6a82784dfbd9462c91f6cda5d 100644 (file)
--- a/src/gromacs/gmxana/gmx_msd.c
+++ b/src/gromacs/gmxana/gmx_msd.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -41,7 +41,6 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
@@ -213,7 +212,7 @@ static void corr_print(t_corr *curr, gmx_bool bTen, const char *fn, const char *
         }
         fprintf(out, "\n");
     }
-    gmx_ffclose(out);
+    xvgrclose(out);
 }
 
 /* called from corr_loop, to do the main calculations */
@@ -607,7 +606,7 @@ void printmol(t_corr *curr, const char *fn,
             }
         }
     }
-    gmx_ffclose(out);
+    xvgrclose(out);
     do_view(oenv, fn, "-graphtype bar");
 
     /* Compute variance, stddev and error */
@@ -1065,7 +1064,7 @@ int gmx_msd(int argc, char *argv[])
         "Note that this diffusion coefficient and error estimate are only",
         "accurate when the MSD is completely linear between",
         "[TT]-beginfit[tt] and [TT]-endfit[tt].[PAR]",
-        "Option [TT]-pdb[tt] writes a [TT].pdb[tt] file with the coordinates of the frame",
+        "Option [TT]-pdb[tt] writes a [REF].pdb[ref] file with the coordinates of the frame",
         "at time [TT]-tpdb[tt] with in the B-factor field the square root of",
         "the diffusion coefficient of the molecule.",
         "This option implies option [TT]-mol[tt]."