Hello, I have been trying perform a molecular dynamics using GROMACS. The idea is to simulate a system with the Human FABP2 and palmitic acid. My simulation is based on this tutorial. After about 5 nanoseconds my structure starts to show a strange behavior, as shows the figure.
Starting structure (left). Structure after 5 nanoseconds of simulation (right).
Does anyone know what causes this problem? I basically followed the tutorial, using the GROMOS96 force field. I suspect that this kind of behavior is called 'blowing up', although I am not sure and want to hear the opinion from more experienced bioinformaticians.