[gmx-users] About g_traj, plotting displacement

[Justin A. Lemkul]

Kiwoong Kim wrote:
> Hi,
> 
> 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?

Likely the manner in which the data sets were plotted.  Use a text editor to 
confirm that there are 6 data sets in traj.xvg, then if you find what you expect:

xmgrace -nxy traj.xvg

Otherwise, there may be some problem such that only 1 data set is produced, but 
I have never seen that happen.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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