[gmx-users] About g_traj, plotting displacement

Kiwoong Kim ilmarekw at gmail.com
Mon Jan 16 14:15:27 CET 2012


I'm trying to plot the displacements in z-coordinate of each particle
belonging to some index group using g_traj.

I typed below thing in prompt

g_traj -f md_0_2_nvt.xtc -s md_0_2_nvt.tpr -n index_traj.ndx -nox -noy -b 0
-e 50 -ox traj -w -xvg xmgrace

There are 6 atoms in the desired index group.

Although I selected the desired index group (let assume it is 1, 2, 3, 4,
5, 6 labelled) atoms, the g_traj only plots the displacement of first atom
in index group (i.e., the displacement of atom 1 but not 2, 3, 4, 5, 6).

I want to plot the displacements of all atoms (1 - 6).

How do I have to do???

What things is incorrect?

Have a good day :)
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