I’m having problems with 1-2, 1-3 and 1-4 special bonds. In my simulation I have 2 molecules and I want to switch off all the special bonds (0 0 0) for one molecule while switch on all the special bonds ( 1.0 1.0 1.0) for the another ( in the same simulation). I don’t know how to do it because seems that special bonds is set for all the simulation and not set for some. I’m waiting any suggestion. Hope someone can help me out and thanks in advance for your reply.
The special bonds setting is universal, so it won't do what you want.
You can turn off all pair interactions in one molecule if you put its
atoms in a group and use the neigh_modify exclude molecule command.
If the atom types are different for the 2 molecules, maybe you can
adjust force field parameters differently for different atom types.
Failing that, you'd have to change the code where neighbor lists
are built to skip the special bonds test for a certain molecule.