Hi, On Tue, Feb 23, 2016 at 6:25 AM Raju Lunkad < r.lun...@students.iiserpune.ac.in> wrote:
> Dear Gromacs users, > I am trying to run a simulation but I am getting the error regarding the > domain decomposition. Which error? People often can't help much without precise information. Probably your system is unstable and was http://www.gromacs.org/Documentation/Terminology/Blowing_Up and your "solution" below is just hiding the real problem. I ran the simulation using "rdd" option and it is > running fine. > Kindly tell me whether "-rdd" option will affect my simulation. If yes, > then which values would get affected using "rdd" option. > mdrun has to choose a minimum diameter for the domains in the decomposition for various code to work well. Choosing rdd too small risks that diameter being too small, which means that the simulation might abort if the domain becomes too small for all the atoms in a bonded interaction to be present in one domain (see brief description at gmx mdrun -h). But in practice almost nobody should have any need to change these things. Mark > Best Regards, > Raju Lunkad > -- > 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.
