Hi, I converted a .tpr file to .pdb using editconf. editconf -f md.tpr -o new-md.pdb I visualised new-topol.pdb using pymol. It has the virtual sites. Furthermore, the molecule(s) does not stay in the centre of the box. I need a proper .tpr or .pdb file for analysis. How can these problems fixed? Thanks in advance -- Ahmet Yıldırım