GROMACS version: 2021.5
GROMACS modification: No
Hi, Is there a way to increase the attraction between atoms (atom types) of two different molecules for certain time steps and switch back to normal? Any suggestions would be appreciable.
You could potentially add a biasing potential via the pull code to bring the molecules together, then continue the simulation without the bias.
Thanks for the reply Justin. Actually, I want to perform an SMD simulation by pulling away the molecule from the surface of a nanoparticle. However, the molecule is drifting a lot in the vicinity of the nanoparticle(the surface of the nanoparticle is charged due to the negatively charged COO- groups attached to the aromatic carbons of the nanoparticle), hence want to induce an attraction between the aromatic carbons of the nanoparticle and the molecule for certain steps and then start to pull the molecule away from its surface. Does it mean to push the molecule towards the surface of the nanoparticle by adding a biasing potential and then pull away?
What you’re talking about sounds like trying to layer ad hoc force field modifications onto a biasing potential. I think that’s unwise. If you can’t force the molecules close together to adopt some intermolecular distances, there’s probably a physically justifiable reason for that. If you still want to smash things together, use a stiffer force constant in the biasing potential.