[gmx-users] PBC

[Alex]

Dear Gromacs user,

I want to study the interaction between a nanoparticle(5 nm diameter) and
some heptapeptide around the nanoparticle in aqueous solution. I put
the nanoparticle
in the center of a box and the rest are around it.
I was wondering if I should use PBC (periodic boundary condition) in such a
system? What is the advantage of the using PBC here?

The disadvantage of using PBC here is that a very big box should be used to
avoid interaction between a peptide and another peptide in the adjacent
cell.

Regards,
Alex