[gmx-users] MDRUN warning during minimization

[Agnivo Gosai]

Dear all,

I used ACPYPE to create the topology using GAFF for two small molecules and
then merged everything with the protein topology built using pdb2gmx (
version 4.6.7 and AMBER99SB) and proceeded for simulation.

At the start of energy minimization this was observed :

WARNING: Listed nonbonded interaction between particles 800 and 807
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.

I am seeing this for the 1st time , kindly help in understanding.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.