[gmx-users] Dummy atoms flopping everywhere

[Raphaël Robidas]

I am doing a free energy perturbation calculation on a protein-ligand
system. I am going from a topology A which has a benzyloxy group to a
topology B which only has a methoxy group. My problem is that when lambda =
1, the simulation crashes because the benzyloxy group is flopping around
too fast, since it has no mass nor collision. I am wondering that the best
way to deal with this would be.

Using restraints would be an option, but I don't need to restrain my ligand
otherwise, so it would be desirable to avoid restraints overall. Could a
second topology without the dummy atoms be used just when lambda = 1 or it
won't be compatible with the rest of the simulations?

Thank you!