GROMACS version: 2019
GROMACS modification: No
I am calculating the free energy of solvation for the cofactor in the protein. I do the very same thing as in the gromacs tutorial for Methane in Water.
I run md trajectories for several intermediate states (lambda). The trajectories with integral charge (i.e. for the charge=1, and for the charge=0 with varying vdw parameters) are ok.
All the other trajectories with cofactor q = 0.875, 0.75, …, 0.125 crash with the following mistake:
WARNING: Listed nonbonded interaction between particles 4197 and 4207
at distance 47.559 which is larger than the table limit 2.200 nm.
I do not know how this could happen, it looks like the PME artifact, because the distance is ok, and the system did not blow up.
Maybe I should insert some modifications in the .mdp parameters?
Thank you in advance,