[gmx-users] dimer split

xy21hb xy21hb at 163.com
Thu Nov 5 17:12:40 CET 2015

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.



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