Hello GROMACS users, I am running NVT alchemical free energy simulations (change in atom number, bonding, etc.). These simulations appear to go well at all lambda values below 1.0 (no errors and the resulting trajectories show no unusual behaviour). At lambda=1.0, the system returns an error before or during the first step:
" *WARNING: Listed nonbonded interaction between particles 376 and 384 at distance 4.655 which is larger than the table limit 2.500 nm. This is likely either a 1,4 interaction, or a listed interaction insidea 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 willonly see this message once, even if it occurs for several interactions.IMPORTANT: This should not happen in a stable simulation, so there isprobably something wrong with your system. Only change the table-extensiondistance in the mdp file if you are really sure that is the reason.*" However the same system (input structure + topology + mdp-settings) will minimize without any issue at same lambda=1.0 setting. If I increase the table-extension distance to 4.0 nm, the distance reported in the error gets very large: " *WARNING: Listed nonbonded interaction between particles 541 and 554 at distance 183739120.000 which is larger than the table limit 5.500 nm.*" I am not sure what is going wrong. Best, Eric -- 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.