Collapse of polymers after annealing

[Narges]

GROMACS version:2022.3
GROMACS modification: Yes/No
Hi there,

After doing simulated stepwise annealing, the system collapsed.
In the first picture, the temperature increased using stepwise annealing. However, when using the same mdp file to decrease the temperature, the system collapsed.

I would be grateful if anyone could guide me in finding the problem.

[JKS]

This looks like just a formatting issue where in the latter case GROMACS inserted all the atoms into the simulation box. You can convert between different treatments of the periodic boundary with “gmx trjconv -pbc whole …”