During Energy minimization error "Listed nonbonded interaction between particles 4778 and 4797 at d"

User discussions
1

NOTE: The number of threads is not equal to the number of (logical) cores
and the -pin option is set to auto: will not pin threads to cores.
This can lead to significant performance degradation.
Consider using -pin on (and -pinoffset in case you run multiple jobs).

Steepest Descents:
Tolerance (Fmax) = 1.00000e+02
Number of steps = 50000

WARNING: Listed nonbonded interaction between particles 4778 and 4797
at distance 5.375 which is larger than the table limit 2.200 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. Please help me

2

Try visualizing the system to figure out what’s going on with those atoms specifically, it’s hard to advise without knowing what you’re trying to simulate