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

Mark Abraham mark.j.abraham at gmail.com
Mon Apr 16 20:57:58 CEST 2018


Make sure your particles have vdw on before you add charge to them. That's
usually the cause of this problem.


On Mon, Apr 16, 2018, 20:51 faride badalkhani <farideh.khamseh at gmail.com>

>  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
> error:
> 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?
> Best.
> Farideh
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