[gmx-users] CNT using g_x2top

Mark Abraham mark.j.abraham at gmail.com
Wed Feb 3 17:50:16 CET 2016

If a single domain doesn't work, then surely your topology or starting
configuration is broken. Start with the simplest system you fan think of!


On Wed, 3 Feb 2016 17:23 soumadwip ghosh <soumadwipghosh at gmail.com> wrote:

> Hi,
>    previously I had a query about making the topology of CNT using g_x2top
> in connection with charmm force field. I have followed Justin's advice and
> was able to generate a 9X9 SWCNT in charmm which I want to simulate with a
> single stranded DNA.  During energy minimization I got this error.
> Reading file em.tpr, VERSION 4.5.6 (single precision)
> Starting 80 threads
> There were 36 inconsistent shifts. Check your topology
> There were 36 inconsistent shifts. Check your topology
> Will use 56 particle-particle and 24 PME only nodes
> This is a guess, check the performance at the end of the log file
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.6
> Source code file: domdec.c, line: 6436
> Fatal error:
> There is no domain decomposition for 56 nodes that is compatible with the
> given box and a minimum cell size of 8.21617 nm
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> Is there a problem with the topology or the gromacs 4.5.6 is unable to
> perform the domain decomposition? If the second is the case can I play
> around with mdrun options to get rid of this. I have seen this question
> posted on the forum multiple times but I dint get any idea of
> troubleshooting it in my case. I tried playing with -nt 1 in which mdrun
> prints a number of .pdb files and the output.gro file contains a broken
> CNT. I have attaced the log file, the cnt.itp file and the minim.mdp file.
> Please let me know if the problem can be settled or the cnt.top itself is
> faulty.
> https://drive.google.com/file/d/0B7SBnQ5YXQSLd1d1cGtSRGZkUE0/view?usp=sharing
> for
> the em.log file
> https://drive.google.com/file/d/0B7SBnQ5YXQSLWjFab1NIMmFiQVk/view?usp=sharing
> for
> the cnt.itp file and
> https://drive.google.com/file/d/0B7SBnQ5YXQSLd3gtRFFrTTA4Wlk/view?usp=sharing
> for
> the minim.mdp file.
> Any kind of help will be hugely appreciated.
> Regards,
> Soumadwip Ghosh
> Senior Research Fellow
> India
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