[gmx-users] Question about "gmx traj" command

[Justin Lemkul]

On 10/16/17 9:36 AM, Chang Woon Jang wrote:
> Dear Gromacs Users,
>
>      I have a question about the gmx traj in order to calculate the force
> components.
>
> I used the following command. > gmx traj -f topol_new.trr -s topol_new.tpr
> -af force_all_z_l9.xvg -z yes
>
> It produced "force_all_z_l9.xvg" file. In the file, there are four columns.
> The first column should be the atom ID.
>
> My question is what is the rest of columns? For example, some of the values
> are negative and the other values are positive.
>
> -z yes means the plot of Z-component in the manual. I do not know what the
> exact meaning of three columns. Would you please give me a comment on that?

You're getting (x,y,z) because you haven't turned them off (note from 
the help info that all dimensions are on by default).

All you need is:

gmx traj ... -nox -noy -z

-Justin

> Thank you.
>
>
> # This file was created Mon Oct 16 21:53:33 2017
> # Created by:
> #        :-) GROMACS - gmx traj, 2016.4-dev-20170620-8d2584c-unknown (-:
> #
> # Executable:  /home/chang/Packages/votca/bin/gmx
> # Data prefix:  /home/chang/Packages/votca
> # Working dir:  /home/chang/2017_NU_PROJECT/1_FIRST_PROJECT/1_Less_5Million/
> 5_REVERSED_ATOMISTIC_TEST/1_Lambda_9/1_TENSION/1_SR10e8_l9_
> 300K/ANALYSIS/7_Force_Component
> # Command line:
> #  gmx traj -f topol_new.trr -s topol_new.tpr -af force_all_z_l9.xvg -z yes
> # gmx traj is part of G R O M A C S:
> #
> # Gromacs Runs One Microsecond At Cannonball Speeds
> #
> @    title "average force"
> @    xaxis  label "Atom"
> @    yaxis  label "Spatial component"
> @TYPE xy
> 1        -11.866      42.002      29.565
> 2          22.660    -11.028    -21.749
> 3          -0.232      -3.681      4.181
> 4          -9.308    -31.931    -22.545
> 5        -27.221    -21.572      7.099
> 6          11.648      4.523      -8.757
> 7          32.491      0.888      17.891
>
>
> Best regards,
> Changwoon Jang

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================