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

[Mark Abraham]

Hi,

I've now proposed to change y axis label to "Spatial component" which is
hopefully more clear. (The same code is also used for -af, so the text
needs to be general.)

Mark

On Tue, Mar 7, 2017 at 11:10 AM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Yes, those are the components of the average velocities.
>
> Mark
>
> On Tue, Mar 7, 2017 at 10:43 AM Kamps, M. <m.kamps at student.rug.nl> wrote:
>
> 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?)
>
> Mark
>
>
>
>
>
> > 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
> --
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