Dear All users,
I have performed an NVT simulation. My system have been equilibrated and now I want to use the
equilibrated system for another simulation. I have extracted a pdb file from VMD and final frame but
I realized that some molecules are located out of my box and it is not good for following run.
I have saved wrapped and unwrapped trajectories but I could not get a right pdb file which is
restricted by initial boundaries. Is it possible to get that? Is there any post processing?