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To extract the force as in the title I used the gmx trjconv command like below.

gmx trjconv -f alad.trr -s alad.tpr -n alad.ndx -pbc mol -novel -force -o alad.gro

However, the force was not extracted in alad.gro file. Of course, I got the coordinates and the force at equal intervals when getting the alad.trr file.

Another way, I used gmx traj command to get force.

gmx traj -f alad.trr -s alad.tpr -n alad.ndx -pbc -mol -ox coordi.xvg -of force.xvg

However, the force obtained from force.xvg didn't look like the value I wanted.

So, how do I get the force of molecules put in a single periodic box?

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  • $\begingroup$ Could you include a figure showing force.xvg, and a better description of what it is exactly that you would like to measure, and why you think the output is not correct. $\endgroup$
    – Bdrs
    Commented Mar 2, 2020 at 15:45
  • $\begingroup$ However, I'm still wondering why coordinates of alad gro and coori.xvg are not same. $\endgroup$
    – Yeonju
    Commented Mar 5, 2020 at 11:49
  • $\begingroup$ I solved the problem. As gmx trjconv -pbc mol option only make molecules translate, the cooridinates obtained from alad.gro can correspond to forces obtained from gmx traj -f alad.trr -s alad.tpr -n alad.ndx -of force-dump.xvg(same results using gmx dump command). However, coordinates of coordi.xvg doesn't match with alad.gro . Also I couldn't trust force.xvg. whether the data is correct is tested by my own work ouput. So it's hard to say simple.. $\endgroup$
    – Yeonju
    Commented Mar 5, 2020 at 11:52
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    $\begingroup$ There is a proposal for a Stack Exchange site for Materials Modeling which is currently in the commitment phase. There are a lot of experts currently there and questions like these would get more activity there. It would be great if you could help building the site by committing to the proposal. $\endgroup$
    – rashid
    Commented Mar 5, 2020 at 11:59

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I solved the problem. As gmx trjconv -pbc mol option only make molecules translate, the cooridinates obtained from alad.gro can correspond to forces obtained from gmx traj -f alad.trr -s alad.tpr -n alad.ndx -of force-dump.xvg.

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