GROMACS version: 2021.2 GROMACS modification: No I am running a MARTINI CG simulation using MARTINI V2. The system comprises of a macromolecule with over 6000 CG beads and a solute with 150+ beads, both in 500K water beads. When I apply position restraints on all beads of the macromolecule and run NPT using Berendsen barostat the water does not return to the cubic box shape even …

GROMACS version: 2019 GROMACS modification: No I have been running a simulation with free-energy coupling, but realised that for lambda=1, which in my case is the end state with interactions fully turned on, the results where different compared to a regular MD run without the free-energy coupling (see attached ion-water RDFs). These are rather long MD runs (~30ns), and even t…