Thanks for the reply. Recently, I came across this response made by you on the Researchgate website.
You need several iterations of trjconv. Using -pbc whole is just the first step, and has nothing to do with the fact that there are multiple oxalates; it just corrects any molecules that have “broken” across PBC. Then invoke trjconv -pbc nojump (you said yourself the molecules are jumping across boundaries), then -pbc mol to put everything back in the box.
Would it be okay to apply the correction as follows:
gmx trjconv -s em.tpr -f polymer.xtc -o polymer.whole.xtc -pbc whole
gmx trjconv -s em.tpr -f polymer.whole.xtc -o polymer.whole.nojump.xtc -pbc nojump
gmx trjconv -s em.tpr -f polymer.whole.nojump.xtc -o polymer.whole.nojump.mol.xtc -pbc mol
Will applying wrong corrections (molecule not inside the box) affect the calculation from gmx rdf?