13 February 2020 1 5K Report

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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