Dear all,

I have a system consisting on a polymer chain solvated in water. I just ran in standalone mode a really long NPT simulation that took a few days. To check how the simulation was going I downloaded the trajectory at different times while it was running. I plotted the MSD curve for the polymer chain each time I downloaded the new trajectory (just the same as the old one but more frames). When I compare the MSD curves calculated from these "different" trajectories (they are the same one but just different duration) I find that the MSD curves are very different when they should be basically the same. I am really puzzled by this result so I would appreciate any insight anybody can offer.

Thanks!