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 7d30ccce8eabcde7bbbacfca4091deb2ca2bbbfd..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]",
 
@@ -579,10 +578,12 @@ int gmx_density(int argc, char *argv[])
         "Densities are in kg/m^3, and number densities or electron densities can also be",
         "calculated. For electron densities, a file describing the number of",
         "electrons for each type of atom should be provided using [TT]-ei[tt].",
-        "It should look like:[BR]",
-        "   [TT]2[tt][BR]",
-        "   [TT]atomname = nrelectrons[tt][BR]",
-        "   [TT]atomname = nrelectrons[tt][BR]",
+        "It should look like::",
+        "",
+        "   2",
+        "   atomname = nrelectrons",
+        "   atomname = nrelectrons",
+        "",
         "The first line contains the number of lines to read from the file.",
         "There should be one line for each unique atom name in your system.",
         "The number of electrons for each atom is modified by its atomic",
@@ -596,7 +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",