I have a coarse-grained particle (bead) that I want to keep off the plane from the plane of other beads which form like a 2D plane. Do people employ improper dihedral for this or any other bonded parameters I can look into? Thanks.
It is very difficult to say how you should do what you want ("keep a bead off a plane of other beads") without knowing why you want to do so.
So, concretely, let's say I'm modelling a lipid bilayer, and I am modelling a small molecule in solution on one side of it, and I don't want it to pass through the bilayer. (Unfortunately, the advice I give in this scenario might be completely irrelevant to your application -- but you must give more detail to receive more detailed useful advice.)
There are one of two valid reasons I might want to stop this small molecule from passing through the lipid bilayer:
- I might want this on physical grounds. Maybe we know experimentally that this molecule does not actually pass through cell membranes, but I'm seeing permeation in my simulation.
- I might want this on mathematical grounds. That is, the molecule does pass through the cell membrane (both experimentally and in simulation), but I want to, say, sample the free energy landscape of membrane passage so that I can compare it to another small molecule (to compare between drug candidates, let's say).
These two reasons require two different responses.
If I want the small molecule to not pass the lipid bilayer for physical reasons, then my model must include a similar physical mechanism -- that is, the lipid headgroups should cohere enough to each other and interact repulsively enough with the small molecule that the cost of permeation is too high.
- Note that this interaction must be defined entirely in terms of the local molecule-lipid headgroup potential, and my molecule is not allowed to "know" where it is in the simulation box or relative to the membrane plane (since, in an experiment, molecules do not "know" how near or far they are from a membrane outside of local interactions either).
If I want the small molecule to not pass the lipid bilayer for mathematical reasons, then I should impose a well-defined (and preferably very simple) mathematical additional force on the molecule.
- In this case, I can use the molecule's distance from the lipid bilayer as an input factor for calculating the force (so, for example, I might impose a harmonic restraint on the z-distance between the small molecule's center of mass and the lipid headgroups' average z).
- Note that this requires that I can eventually convert the mathematically-biased simulation back into experimentally-relevant results, which will control the mathematical formula I use (for example, it's much easier to calculate some quantities for a harmonic potential than for any other arbitrarily-shaped potential).
I hope this helps. Note that in both cases it's not really conventional to impose "improper" or "dihedral" interactions, which are usually used for modelling intra-molecular interactions such as backbone torsions.