[gmx-users] Meaning of columns in .xvg output file

Kamps, M. m.kamps at student.rug.nl
Tue Mar 7 10:43:07 CET 2017

Dear Justin,

Thank you for you reply. The header of my .xvg file is:

# This file was created Mon Mar  6 14:32:28 2017
# Created by:
#                       :-) GROMACS - gmx traj, 2016.1 (-:
# Executable:   /usr/local/gromacs/bin/gmx
# Data prefix:  /usr/local/gromacs
# Working dir:  /local/Data/Nozzle/19./4.MD Acceleration
# Command line:
#   gmx traj -f md_acc.trr -s md_acc.tpr -b 7.5 -e 8.5 -n 1.ndx -av plot1.xvg
# gmx traj is part of G R O M A C S:
# GROtesk MACabre and Sinister
@    title "average velocity"
@    xaxis  label "Atom"
@    yaxis  label ""
@TYPE xy
1           0.015       0.354      -0.083
2          -0.242      -0.053       0.026

Where the counter obviously continues to larger values. As you can see
the x-axis contains the atom number (same as the first column; the
counter), while the second column is plotted as the y-values. The
y-axis remains empty.
The .xyz file is created via gmx select to select multiple residue
groups, after which I am interested in the average velocity of the
selected groups. Is it possible that the three colums represent the
average velocity in each of the three directions (XYZ?)


> On 3/6/17 5:36 AM, Kamps, M. wrote:
>> Dear gmx-users,
>> I've got a small question of which I can't find the answer. I have a
>> simulation where I want to calculate the average velocity of certain
>> particles. I've created an output .xvg file via the command:
>> gmx traj -f input.trr -s input.tpr -n input.ndx -av output.xvg
>> My output, is as requested an .xvg file which can be plotted in xmgrace.
>> However, when opening this .xvg file with a text-editor, it has four
>> columns of output, of which only the first two columns will be used by
>> xmgrace. The first column is a simple counter, however the other three
> You can plot everything with xmgrace -nxy output.xvg
>> columns all contain values. Supposedly, the second column (column 2 of
>> 4) contains the average velocities. My question: What are the values
>> in column 3 and 4?
> What do the labels in the header of the file say, or alternatively, what does
> the legend say when you plot with the above command?
> -Justin

More information about the gromacs.org_gmx-users mailing list