GROMACS version:
GROMACS modification: Yes/No
i have used trjconv -pbc nojump command but the water molecules in my system has started to diffuse.
i am unable to understand why this is happening.
That’s the whole point of the nojump option, it avoids jumps to other PBC images. As a result, any atom/molecule can be seen to “diffuse into” neighboring images, which are in fact identical to the central one. This is, however, much more convenient for e.g. calculating diffusion constants. And yeah, I know it’s tricky, it takes a while to start thinking in PBC terms for everyone.
Thank you so much. I didn’t completely understand what nojump meant. i assume it just stops the jumps of the protein molecule.