How to make 2 atom groups see each other despite cutoff?

User discussions
1

GROMACS version: 2020.1
GROMACS modification: No

Hi all,
I am running simulations of 2 small molecules in different mixtures of solvents.
My small molecules are 6 membered aromatic rings, which I would expect to stack together at least for part of the simulation, but over 100 ns their centroids never seem to come within 0.5 nm of each other (most of the time they are at ~3.5 nm).

I suspect this may be because they move faster than the neighbour list is updated, meaning that every time the neighbour list is updated, my molecules are unlikely to be close enough to see each other. I have tried decreasing nstlist, but then got a note from grompp saying that nstlist has no effect on accuracy. I’d rather not increase the cutoff, as I have a very large number of solvent molecules and I would expect it to make my calculations really slow.

Is there any way to enforce the calculation of interactions between two (or more) specific atom groups, regardless of cutoff/neighbour list?

Thanks!

2

Hi,
One reason of the behavior that you observed can be that your molecules diffuse very slowly and 100 ns are not enough. Another reason can be that the force field is not well-tuned
In alternative to standard MD, you can run a pulling simulation using a reaction coordinate the distance between the molecules and apply a pull-rate such as that the two systems are “pulling” closer. See more Molecular dynamics parameters (.mdp options) — GROMACS 2021 documentation.
This will allow to understand how they will interact once they come closer to each other, but it will not provide information on spontaneous aggregation.
Best regards
Alessandra