[gmx-users] disabling nonbonded interactions between two specific groups

[Irem Altan]

Hi all,

Is it possible to disable nonbonded interactions between two specific groups? What I would like to do is a type of alchemical transformation to calculate free energies. Are  the following steps possible within Gromacs?

- to have a molecule represented with standard force fields AND a Lennard Jones particle superimposed on it
- the molecules interact with each other and the LJ particles interact with each other but the molecules don’t interact with LJ particles
- across multiple simulations, the interaction energy of one species gets turned off gradually

For the last part, is it possible to weaken the bonded interactions of the molecules and not have them fall apart by restraining the bond lengths with lincs? If so, can something similar be done to the dihedrals?

Best,
Irem