I have a very basic question of doing vacuum md simulation of my polymer molecule. Shall I put the position restraint on my polymer (solute) molecule while doing vacuum MD simulation ? Is the pbc set to no with all cut-off's set to zero during vacuum simulation of a solute ? In my case solute is polymer chains. While removing position restraint on my molecule with no pbc condition in vacuum simulations, I am observing my solute flying out outside the box and this is obvious after starting of nvt run. Why ? Please calrify