I have two polymer molecules with benzene rings as a part of them. I would like to understand how the interactions between them influences the solvability of the polymer in a non-aqeous solvent. I understand that it's termed under pi-stacking. Is it just about the distances between the two rings? If so, should I just calculate the distance between the centres of the two rings at different time instants?

Can someone explain how to qualitatively and quantitatively understand pi-pi stacking using GROMACS or any other tools?


I fear that GROMACS may not be able to capture the interaction you are talking about (If someone is an expert in GROMACS please correct me). This sort of pi-stacking interaction will likely result in either a charge transfer (if asymmetric) or some sort of pi-pi bonding interaction that a forcefield is unlikely to capture.

If you took a snapshot of the MD and looked at a DFT level you may see some favorable interactions occurring, this might be a good use of QM/MM calculations. In a DFT calculation, you can quantify the charge transfer and orbital overlaps.

You should see if your forcefield is validated to reproduce pi-pi interactions as a first step.

  • $\begingroup$ I agree with @Tristan. Most famous force fields doesn't have a explicit term specifying pi-pi interactions. This interactions come under derived interactions, which are a combination of both electrostatic and van der Waals interactions. For example, CHARMFF does predict this pi - pi interactions I guess, atleast I saw the attractive energies between benzene rings when they are at a proper distance and alignment. $\endgroup$
    – Vasista
    May 18 at 7:51

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