I am calculating the PMF of two atoms in a 161616 box. Atomic information is stored in data file. There are 4096 atoms in my box. I used fix smd command to calculate the PMF. The initial distance between atoms is 2.7. But the result showed that the distance between the two atoms was 184. After I changed the atoms’ number. But the results are same. I am confused about the result. I apologize in advance if the question is stupid but any suggestions would be appreciable.

I am calculating the PMF of two atoms in a 16*16*16 box. Atomic information is stored in data file. There are 4096 atoms in my box. I used fix smd command to calculate the PMF. The initial distance between atoms is 2.7. But the result showed that the distance between the two atoms was 184. After I changed the atoms’ number. But the results are same. I am confused about the result. I apologize in advance if the question is stupid but any suggestions would be appreciable.

there is not enough information here to make any specific
recommendation. my first suspicion would be, that there is that you
may need to reset your image flags, assuming that this is an atomic
and not molecular system.