To get position of a molecule without jump

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Hi alevilla, your suggestion now solves my issue. I would write here so that it would be helpful if someone stuck with same problem.
I had used following gromacs codes in order to get the coordinates of molecule A without pbc or jump:

  1. gmx trjconv -f nvt.xtc -s nvt.tpr -pbc no jump -o nvt_nojump.xtc -tu ns
  2. gmx trajectory -f nvt_nojump.xtc -s nvt.tpr -ox position_moleculeA.xvg -seltype mol_com
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