[gmx-users] extract the coordinate by using traj command for sphere system

[gozde ergin]

Dear all,

In order to calculate the osmotic pressure I would like to extract the coordinate of my atoms by using g_traj command. 

Before my box was cubic and by using

gmx_mpi traj -f nvt.trr -s nvt.tpr -n index.ndx -ox coord-atoms.xvg -nox -noy

I was getting coordinate of all of my atoms in the system. So this was working fine.

However now my system is sphere and I again want to extract the coordinate file of all my atom. However if I use: 

gmx_mpi traj -f nvt.trr -s nvt.tpr -n index.ndx -ox coord-atoms.xvg -com

I only get the coordinate X,Y and Z component not all atoms coordinates.

Do you have any hint how to extract the atoms coordinate files in gromacs for sphere system?

Thanks in advance.