GROMACS version: 4.6.5
GROMACS modification: No
I am running a simulation of a carbon nanotube immersed in water. The simulation causes error whenever I attach hydrogen to the edges of the tube, otherwise, it works just fine. What can I do to solve this? The error message is displayed here.
WARNING: Listed nonbonded interaction between particles 1303 and 1308
at distance 3f which is larger than the table limit 3f 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.
1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs