[gmx-users] CNT using g_x2top

soumadwip ghosh soumadwipghosh at gmail.com
Wed Feb 3 17:22:49 CET 2016

   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

the em.log file

the cnt.itp file and

the minim.mdp file.

Any kind of help will be hugely appreciated.

Soumadwip Ghosh
Senior Research Fellow

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