[gmx-users] box volume

[soumadwip ghosh]

Hi,
    beg me pardon 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.

Soumadwip Ghosh
Research Fellow
IITB
Mumbai
India