I want to keep track of the position of my polymer chain in a pbc box. Since I cannot create a box of very large dimension, and I don't want the polymer chain to cross the boundary hence the best way to deal with this problem is regularly move my box wrt the center of mass of my polymer chain. Is it possible to regularly update the box bounds?
Just use fix spring on the polymer with a reasonably weak force
constant and it won't drift anymore.
I want to track the drift.
Or, depending on what you want to achieve exactly, you can also
recenter the box on the polymer center of mass every time step, using
fix recenter on the group polymer, and keyword shift all:
The question is, why don't you want the polymer to cross the
boundaries, as they have no physical meaning if you are using PBC?
Then why don’t you write out the unwrapped coordinates when dumping them to a file?
No need to mess with the box boundaries for that.