GROMACS version:2022.3
GROMACS modification: No
I am new to gromacs and trying to do some simulations.
I modeled the structure file and created some bonds. I am pretty sure the bondings were created between the right atoms, but the relative distance might not be in the normal range.
The bonding broke after solvation (before adding ions), and it was messed up among the residues around it. Would it be because of the distance? Are there any parameters I could use to keep the original bonding potentially? I was hoping the distance and angles would be fixed after the minimization.
However, after the minimization, the water box changed shape, one subunit flew out of the box, and there were some very weird super-long bonds shown in the structure.
(for the mdp files, I mostly followed the lysozyme in water tutorial)
I have no idea about what is going on. Any suggestion is very much appreciated!