I noticed the preprint “Neighbor List Artifacts in Molecular Dynamics Simulations”(Neighbor List Artifacts in Molecular Dynamics Simulations | Theoretical and Computational Chemistry | ChemRxiv | Cambridge Open Engage) from the Hummer group discussing how there are issues in GROMACS defaults resulting in short outer cutoffs and infrequent neighbor list updates that lead to missing long-range attractive Lennard-Jones interactions, as well as small but systematic imbalances in the apparent pressure tensor then induce unphysical asymmetric box deformations that crumple the membrane. Have people seen this yet? I didn’t see any other post in the developer forum. Does it appear to indeed be an issue, or did they get something wrong?
This is an actual issue. But, as far as I have seen, it is only leads to measurable effects in systems without electrostatics. Thus in practice this is only an issue for coarse-grained systems and very hydrophobic polymers. When there are some electrostatic interactions present, these will lead to a sufficient Verlet buffer and/or sufficiently short pair list lifetime such that the missing LJ interactions are negligible. So nearly all atomistic simulations are unaffected by this.
I have a change ready that prints the average pressure error to the log file. We should likely add a warning when using semi-isotropic or anisotropic pressure coupling. For the 2024 release we need to find the best way to always set a sufficient buffer.