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

[Mark Abraham]

Hi,

Force is a vector, yes. And its units are not kcal/mol nm in GROMACS. See
chapter 2 of the reference manual.

Mark

On Tue, Oct 17, 2017 at 9:00 AM Chang Woon Jang <changwoonjang at gmail.com>
wrote:

> Dear Justin,
>
>     Thank you for your help. One more question is that there are positive
> and negative values. Does this mean that the forces are written as
> vector values? For example, the value of -40 means negative Z direction
> with 40 kcal/mol nm ?
>
> Thank you.
>
> Best regards,
> Changwoon Jang
>
> On Mon, Oct 16, 2017 at 10:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > 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
> >
> > ==================================================
> >
> > --
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