Handling of PBCs with multiple peptides

User discussions
1

GROMACS version: 2024.3
GROMACS modification: No
Hello,
I am intending to run simulations with multiple copies of a peptide chain in one box. Does anyone have tips of PBC corrections before analysis when dealing with mulitple chains in a simulation box?

Thank you.

2

Does it work with gmx trjconv -pbc whole, followed by gmx trjconv -pbc nojump?

3

I will try it out. Thank you!