[gmx-users] Question about "gmx traj" command
jalemkul at vt.edu
Mon Oct 16 15:38:14 CEST 2017
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
> 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
> 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/
> # 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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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