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
--
========================================
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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