Yeah I did that and there was no error, cheers. I did the same thing a week a go for a united atom model of hexane, I did not get the warning then even though the molecules were still broken. Peculiar?
Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Then is this a bug?, or do I have to have a box in which all the >> molecules are whole. Does that not defeat the purpose of having a >> periodic box? >> > > In a sense, maybe this is a grompp bug, in that it does not account > for periodicity. There is no harm in using this run input file, > though, which you can verify by making the molecules whole and then > re-running grompp. You shouldn't see the same error. > > -Justin > >> Gavin >> Justin A. Lemkul wrote: >>> >>> Gavin Melaugh wrote: >>>> Hi Justin >>>> >>>> By "broken" do you mean split at the edge of the periodic box? If so >>>> then yes. >>>> >>> Then that's your problem. >>> >>> -Justin >>> >>>> Gavin >>>> >>>> Justin A. Lemkul wrote: >>>>> Gavin Melaugh wrote: >>>>>> Hi >>>>>> >>>>>> I have installed the new version of gromacs and so far I only use >>>>>> it as >>>>>> a check when running grompp as it gnerates more information about >>>>>> cut >>>>>> off charge group radii etc. >>>>>> For a system of 256 hexane molecules in a cubic box I get the >>>>>> following >>>>>> error. >>>>>> >>>>>> WARNING 1 [file pbc.mdp]: >>>>>> The sum of the two largest charge group radii (5.231524) is larger >>>>>> than >>>>>> rlist (1.700000) >>>>>> >>>>>> This doesn't even make sense since my as system itself fits in a >>>>>> 3.2 nm >>>>>> cubic box. I am pretty sure my topology is correct. I have seen >>>>>> on the >>>>>> mailing list that there have been problems with this but they >>>>>> have all >>>>>> been for bigger molecules. >>>>>> >>>>> Are any of the molecules broken? That was the exact case just a >>>>> couple of days ago: >>>>> >>>>> http://lists.gromacs.org/pipermail/gmx-users/2011-January/057980.html >>>>> >>>>> -Justin >>>>> >>>>>> Gavin >>>>>> >>>> >> >> > -- 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
