GROMACS version: 2023
GROMACS modification: Yes/No
I have used docked peptide drug complex for simulation in gromacs. i have attached the picture of docked complex below. i generated the topolgy files for drug using acpype and then edited the topology file and added the parameters of my drug into it. however after the simulation of 50ns my drug has distorted it’s shape and drifted away from my peptide. I have attached pictures below. Kinldy help. I am unable to figure out the error.
the second image is after simulation of 50 ns. This is a snapshot at 10 ns.