#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"
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++)
"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]",
"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",