Hi

I performed NVT simulation on a box filled with water with an Au nanowire constrained in the center. My problem is that at the end of the run a large number of water molecules are out of the box. In the pdb file also  the dimensions of some atoms are out of the original box. As long as I know in NVT situation number of molecules are supposed to remain constant in the box. I don’t know if it’s only a graphical matter and the pbc condition is performed automatically or not !. Otherwise, my results like interaction energy can be wrong.

The simulation setup is:

NVT ensemble

Pbc situation

Ewald sum method

T= 300K

Focefield : PCFF

Regards

soheil