GROMACS version:5.1.4 and 2018
GROMACS modification: No
When performing an alchemical calculation of a relatively large molecule, for instance a large hydrocarbon (say icosane Nb Carbons = 20) in water, I get multiple warnings concerning non-bonded interactions (see below)
WARNING: Listed nonbonded interaction between particles x and y
at distance 2.047 which is larger than the table limit 2.000 nm.
This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.
The x and y above can be either both atoms of the hydrocarbon or atoms of the hydrocarbon and water.
The force field I used was OPLS-aa and I tried 2 different versions of gromacs (5.1.4 and 2018).
I am running MD (NPT) and I get no LINCS warnings.
These warnings do not occur if I carry out a “normal” MD (i.e., no decoupling).
For smaller hydrocarbons, even with with 1,4 interactions I did not get such a warning (e.g., dodecane Nb carbons = 12).
The simulations for different lambdas end and it is possible to calculate the free energy afterwards.
Although the warning clearly points out a direct relation with the decoupling approach I am not sure what it means exactly and its consequences.
Increasing table-extension “solves” the problem. However, I do not understand the nature of the problem, and I do not want to simply increase table-extension without understanding the source of it.
Any hint on this would be highly appreciated.
Thanks in advance