GROMACS version: 2023.1
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I have 2 polymer chains in solution and would like to keep a few atoms within a relative distance to each other. For example, chain 1 has atom A and chain 2 has atom B. I would like to keep A and B within, say, 1 nm of each other. One way to do this is to restraint the positions of A and B using position restraints but that can influence the conformation of the polymer chains and does not represent the true nature of the polymer-polymer interaction.
I would like that both the polymer chains coil in solution independently but A and B remain within 1 nm of each other.
Can someone please suggest how to realise this.
Thanks,
Raman