Move read_tps_conf() to confio.h

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

diff --git a/src/gromacs/gmxana/gmx_density.c b/src/gromacs/gmxana/gmx_density.c
index ef83a98a784bece17bfb3943fb9cb708c84c6385..29bd719c4380249654e5134386405de7e8543bce 100644 (file)
--- a/src/gromacs/gmxana/gmx_density.c
+++ b/src/gromacs/gmxana/gmx_density.c
@@ -42,7 +42,6 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
@@ -158,7 +157,7 @@ void center_coords(t_atoms *atoms, atom_id *index_center, int ncenter,
         com[m] /= tmass;
     }
     calc_box_center(ecenterDEF, box, box_center);
-    rvec_sub(box_center, com, shift);
+    rvec_sub(com, box_center, shift);
 
     /* Important - while the center was calculated based on a group, we should move all atoms */
     for (i = 0; (i < atoms->nr); i++)
@@ -565,7 +564,7 @@ int gmx_density(int argc, char *argv[])
         "of an arbitrary group, in absolute box coordinates. If you are calculating",
         "profiles along the Z axis box dimension bZ, output would be from -bZ/2 to",
         "bZ/2 if you center based on the entire system.",
-        "Note that this behaviour has changed in Gromacs 5.0; earlier versions",
+        "Note that this behaviour has changed in GROMACS 5.0; earlier versions",
         "merely performed a static binning in (0,bZ) and shifted the output. Now",
         "we compute the center for each frame and bin in (-bZ/2,bZ/2).[PAR]",
 
@@ -598,7 +597,7 @@ int gmx_density(int argc, char *argv[])
         "The first problem that while both proteins and lipids have low volume",
         "compressibility, lipids have quite high area compressiblity. This means the",
         "shape of the box (thickness and area/lipid) will fluctuate substantially even",
-        "for a fully relaxed system. Since Gromacs places the box between the origin",
+        "for a fully relaxed system. Since GROMACS places the box between the origin",
         "and positive coordinates, this in turn means that a bilayer centered in the",
         "box will move a bit up/down due to these fluctuations, and smear out your",
         "profile. The easiest way to fix this (if you want pressure coupling) is",