Hi Mark, I ran on 48 processors.....the error is:
The X-size of the box (5.312040) times the triclinic skew factor (1.000000) is smaller than the number of DD cells (6) times the smallest allowed cell size (0.885281) Kind regards, chetan ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham [mark.abra...@anu.edu.au] Sent: 27 December 2010 00:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] number of DD cells On 27/12/2010 7:51 AM, Poojari, Chetan wrote: > Hi, > > I am following umbrella sampling tutorial for my membrane protein system. > > While running continuous pulling simulation (mdrun)..... under step five: > Generating Configurations of the tutorial. I get the below error. > > The system ran initially but corrupted very soon with warning " The X-size of > the box (4.800448) times the triclinic skew factor (1.000000) is smaller than > the number of DD cells (4) times the smallest allowed cell size (1.200000) " > > I am using 64 cores with -npme = 16. I haven't set any -dds. > My system box size is 6 x 6 x 12 nm That's a large box deformation... 6nm to 4.8nm. I'd say your system is probably blowing up, and that -dds 0.6 is hiding the symptoms. Try running on fewer processors to see whether when the DD box size is larger whether you get other explosion symptoms. Mark -- 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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ -- 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