GROMACS version: GROMACS 2021.4
GROMACS modification: Yes, with PLUMED-2.7.3 patching
Hi all, I was trying to calculate the solvation free energy of a small simple molecule that is composed of 4 sites using expanded ensemble (couple-intramol = no). The first and the last atom were charged (+0.3 and -0.3, respectively). The distance of these two atoms was about 0.4 nm. rlist was set as 1.0 nm in the mdp file.
The simulation failed within 100 ps with the following error:
Fatal error:
There are 1 perturbed non-bonded pair interactions beyond the pair-list cutoff
of 0.999 nm, which is not supported. This can happen because the system is
unstable or because intra-molecular interactions at long distances are
excluded. If the latter is the case, you can try to increase nstlist or rlist
to avoid this.The error is likely triggered by the use of couple-intramol=no
and the maximal distance in the decoupled molecule exceeding rlist.
I’ve tried to change rlist from 1.0 to 1.15 (with verlet-buffer-tolerance as -1), but the same error occurred:
There are 2 perturbed non-bonded pair interactions beyond the pair-list cutoff
of 1.15 nm ...
(Given my box vector (2.30185 2.30185 1.62765 0.00000 0.00000 0.00000 0.00000 1.15093 1.15093), this is almost the largest rlist that I could use.)
If I understand correctly, this is related to the bug in the current version of GROMACS according to this post: Bugs fixed — GROMACS 2023-dev-20220204-7dec3a3 documentation
In the post, there are following two issues referred:
(1) solvation free energy with couple-intramol set to no - Redmine #3403 (#3403) · Issues · GROMACS / GROMACS · GitLab
(2) Deprecate mdrun-only build (#3808) · Issues · GROMACS / GROMACS · GitLab
However, based on the last message of the first issue above, I’m not sure if the problem has been entirely fixed in the next release. More importantly, I’m wondering if there are any workarounds for users who are using GROMACS 2021.4. (For me, I needed to use GROMACS 2021.4 because that is the newest version of GROMACS that PLUMED can be patched with.)