[gmx-users] WARNING: Listed nonbonded interaction between particles X and Y at distance

faride badalkhani farideh.khamseh at gmail.com
Mon Apr 16 20:51:27 CEST 2018

 Dear all,
I am trying to perform free energy calculations of a small drug in octanol
using the GROMACS 5.1.3 software. I built a box of octanol using the
following command
gmx insert-molecules -ci oct.gro -nmol 125 -box 4 4 4 -o oct_box.gro
Followed by steepest descent minimization, 100 ps each of NVT
and NPT equilibration and 10 ns of production MD. Then, I centered the drug
into the equilibrated box using editconf and performed a same procedure as
the octanol bax to equilibrate the drug-octanol system. All minimization,
equilibration and production simiulations were done without any error and
the plots showd that the system had been equilibrated well. Finally, I
performed the free energy calculations but at MD step I got the following
WARNING: Listed nonbonded interaction between particles X and Y at distance
2.2 which is larger than the table limit 2.2 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.
Could you help me with this problem, please?

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