Hi, Make sure your particles have vdw on before you add charge to them. That's usually the cause of this problem.
Mark On Mon, Apr 16, 2018, 20:51 faride badalkhani <farideh.kham...@gmail.com> wrote: > 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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.