GROMACS version: 2023
GROMACS modification: Yes/No
Hello, I would like to calculate the contacts of hydrophobic interactions in my systems. In a reference article, it was calculated via gromacs: " Hydrophobic interactions were determined by creating a minimum distance contact map using only hydrophobic amino acid sidechains and a cutoff of 0.45 nm."
I am a bit confused about how it was calculated. Is it reasonable to use gmx mindist command in this regard? What would be the command for this? Also, should I use -group option as well? Once I tried to use the -group option, I got the same contact number for each frame. Is not it a bit surprising?