[gmx-users] questions about remove PBC condition from trajectory

[凌未风]

Hello, I have a trajectory and I have a problem to remove PBC condition. 
The problem is I have to small molecules in my system, and I would like to put them in the same box (in the simulation, one of the molecule diffused to another box, and I would like to remove this) and keep them whole. I tried combination of the following two commands:

1, trjconv -f  input.xtc -o output.xtc -s xx.tpr -n index.ndx -pbc nojump  
 2, trjconv -f  input.xtc -o output.xtc -s xx.tpr -n index.ndx -pbc mol

I also tried this:
1, trjconv -f  input.xtc -o output.xtc -s xx.tpr -n index.ndx -pbc nojump  
 2, trjconv -f  input.xtc -o output.xtc -s xx.tpr -n index.ndx -pbc whole

However, I gound after command 1,  one of the molecule still diffused to another box, and after command 2 the two molecules are put back into the same box, but in some frames they are broken again. 
Dose anyone know how to put the two molecules in the same box (not let one molecule diffuse to another box) and keep them whole molecules (not broken)?

I also tried a lot of other combinations, but none of them work. I really appreciate your help. :)

With my best regards, 
RXG