[gmx-users] dimer split

[xy21hb]

Dear all,

I have a two-identical dimer protein, and I am interested in the chain-chain interaction.
However, after long MD, the two chains are separated far from each other though I used PBC.
In fact, the chains should be quite close.

I guess GROMACS treats the chains as A and B, and restrain each individually.
I wonder if there is any way GROMACS  can consider it as a whole, or maybe other solutions.

Thanks,

Yao