|Date: 2018-07-12 16:55|
Sender: Peter Eastman
The PDB format doesn't support varying the box size over a simulation. It only provides one place to store a single box size for the whole trajectory. If you write to a DCD file instead, it will record the current box vectors for each frame.
Remember that a Topology isn't specific to a Simulation. You can create many different Simulations that all use the same Topology, so automatically modifying it would create many potential bugs.