GROMACS version: 2022.1
GROMACS modification: Yes/No
Here post your question Hi, I am using gromacs for coarse-grained simulations. I have some explicit ions inside the box, and a big molecule. Now, I want to make movie using gmx trjconv, and I want both the molecule and ions to be present in the movie at the same time. when I am using -pbc jojump, the molecule remains intact, but the ions seems to continously drifting away throughout the whole movie, so I am not getting a good visual representation, now when I am using any other options like -pbc whole, or -pbc mol, then the ions seems to be confined within a box, but the moleule seems broken in many of the frames, so I cannot get a good movie of my simulation. Can anyone suggest me a way out?