[gmx-users] regarding box volume

[soumadwip ghosh]

Ignore the previous mail.

Hi,
    please excuse me if my question appears very silly to you. I have a
hybrid of a Carbon nanotube and a polymer and I want to study the
unwrapping dynamics of the polymer in presence of a polymer binding agent.
I kept the hybrid inside a triclinic box and am doing simulations in
presence of that binder for 100 ns. The size of the box is around 277 nm3.
Is there a possibility that once the hybrid dissociates the polymer may not
have enough volume to go apart from the CNT and hence affecting the correct
dynamics picture? Should I perform such kind of simulations in a bigger
box? I might be missing out something very fundamental. Your help would be
appreciated.

Sorry if I am asking for much.