Did you follow the link in the error message?
On Wed, Sep 4, 2013 at 7:17 PM, Golshan Hejazi <golshan.hej...@yahoo.com>wrote: > Hi everyone, > > I am simulating a system of paracetamol crystal in ethanol solvent. I used > pdb2gmx to generate the topology and gro file and I minimized the system > using steepest decent. As long as I perform NVT simulations at any > temperature, the simulations goes on! But as soon as I switch from NVT to > NPT, the simulation crashes with the following error: > > I tried to perform NVT at very low temperature, say 50K and then switch to > NPT ... but no WAY! > Can you help me with that? > > Thanks > > Warning: 1-4 interaction between 1361 and 1368 at distance > 10600663849073184.000 which is larger than the 1-4 table size 1.800 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size > > ------------------------------------------------------- > Program mdrun, VERSION 4.5.4 > Source code file: pme.c, line: 538 > > Fatal error: > 9 particles communicated to PME node 0 are more than 2/3 times the cut-off > out of the domain decomposition cell of their charge group in dimension y. > This usually means that your system is not well equilibrated. > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > -- > 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 > -- 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