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

[Chang Woon Jang]

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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