How do I use Lennard-Jones particles in Gromacs to simulate the effect that crowding has on a protein?
Will LJ particles really simulate crowding? Normally one would add more proteins or some kind of viscous co-solvent, like glycerol, from what I’ve seen.
You may need to define a new atom type in ffnonbonded.itp, a residue in the force field .rtp file, then create a dummy coordinate file of one atom (coordinates are arbitrary) to generate the topology and use as input for gmx insert-molecules -ci. After adding the LJ particles, update the topology to reflect how many were added, and proceed with adding water and whatever else your system needs.