GROMACS version: 2021.3
GROMACS modification: Yes/No
Hi, I am relatively new to MD simulations and needed a suggestion as to whether or not I should use -pbc yes while trying to calculate the minimum distance between my protein and its periodic image using gmx mindist?
After obtaining the raw trajectory, I have used gmx trjconv to make molecules whole, remove any jumps, and center the protein inside the box. Since, I have essentially corrected any PBC effects, do I still need to run gmx mindist with -pbc yes option?
Any help in this regard would actually be useful, I’m confused. Thank you in advance!