First of all, thanks to ALL users and developers for your time and help with all my questions.
I using mbtools to run a simulation which contains a large chain of monomers among other molecules.
I want to restart the simulation with different conditions; to save the actual configuration I was using the command: polyBlockWrite "$outputdir/$ident.[format %04d $j].gz" {time box_l npt_p_diff } {id pos type v f molecule}
Then, I used the generated file to restart the simulation. However, when I visualized the snapshots in VMD, there are many bonds spanning along the box simulation. I think this is an effect of the periodic boundary conditions. To fix the problem I tried to fold the positions: polyBlockWrite "$outputdir/$ident.[format %04d $j].gz" {time box_l npt_p_diff } {id folded_position type v f molecule}
But still the same problem.
Does anybody has an idea of how to fix the problem?