Hi all, I'm trying to determine the free energy of solvation for a molecule in n-octanol. I'm separately turning off the Coulomb and Lennard-Jones interactions as instructed in the free energy tutorial. The Lennard-Jones simulations keep on crashing for most values of lambda with the message: Program mdrun, VERSION 4.6.3 Source code file: /home/zidar/gromacs-4.6.3/src/mdlib/domdec_top.c, line: 393
Fatal error: 1 of the 79007 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors - - - I tried using "-noddcheck", "-pd" (separate simulations) but the simulations still fail. The molecule surveyed is not charged (branched hydrocarbon) and I can simulate it using any ensemble without a problem. I'm using CgenFF without adding any new atom types so all the interactions should be properly accounted for. Any advice on how to solve this will be greatly appreciated. I was able to perform free energy simulations of a similar molecule in octanol without any major problem. Thanks, Jernej -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
