[gmx-users] can anyone plx help me with the problem Listed nonbonded interaction between particles 112 and 120 at distance 3f which is larger than the table limit 3f nm.

[Rapunzel Eugene]

I am trying to simulate a protein-ligand interaction. but my mdrun produces this error while running on command:gmx mdrun -v -deffnm em

am getting the following error:
 Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000

WARNING: Listed nonbonded interaction between particles 112 and 120
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.



WARNING: Listed nonbonded interaction between particles 1889 and 1906
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.


Step=    0, Dmax= 1.0e-02 nm, Epot=         -nan Fmax= 6.06156e+13, atom= 3

I will be thankful for your suggestions. Thanking you in advance