Hi, You should use trjconv in 2 steps:
(1) trjconv_d -s md_100ns.tpr -f md_100ns.xtc -o md_100ns_pbc_nojump.xtc -pbc nojump in this step, select system for output (2) trjconv_d -s md_100ns.tpr -f md_100ns_pbc_nojump.xtc -o md_100ns_pbc_mol_center.xtc -pbc mol -center in this step, select solute for centering and system for output. I hope it help you
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