GROMACS version: 2024.5
Dear Gromacs users,
I am attempting to run a solvation free energy calculation of an organic molecule: merocyanine (the molecule contains 42 atoms). I solvated the system in a cubic box (4x4x4) including 1362 tip3p water molecules. I am decoupling the vdw and coulomb terms for alchemical simulations. The distance between the two farthest atom is approximately 1.2 nm.
When I am running the mdrun with gromacs-2024, I am getting the error: “4-non-bonded pair interactions beyond the pair-list cutoff”, but I am not getting that error when I am using gromacs-2018.6. I am using coupl-intramol = no in the mdp file and I changed that to “yes” and now in gromacs-2024 simulations are running.
Is it okay to use coupl-intramol = yes for solvation free energy calculations of a molecule containing 42 atoms? Also does this “non-bonded pair interaction” error have to do anything with gromacs versions as it seems that 2018.6 is working fine but not 2024.5? Any help or suggestions will be highly appreciated, thank you.