[gmx-users] pbc problem

elham tazikeh elham.tazikeh at gmail.com
Wed May 14 13:54:06 CEST 2014

dear gromacs users
i did simulate zinc and copper ion on human growth hormone protein
when i saw my md.gro and md.xtc files by VMD software
i found out my system isn,t in the box(cubic)
i tried to solve this problem by :

trjconv -f md.xtc -s md.tpr -o new.xtc -n index.ndx -pbc mol

but there is this problem,again.
could you please help me

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