[gmx-users] Error during mdrun

soumadwip ghosh soumadwipghosh at gmail.com
Mon Feb 23 15:32:17 CET 2015

Dear all,
             I started an MDrun of Barstar protein in TIP3P water and 8M
urea, neutralized by the required number of counterions. Until the mdrun,
there was no issue with either energy minimization and equilibration steps.
But whenever I want to start MD run, a fatal error shows up saying...

Reading file mdrun_100ns.tpr, VERSION 4.5.6 (single precision)
Starting 80 threads

Will use 70 particle-particle and 10 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 70 nodes that is compatible with the
given box and a minimum cell size of 0.952625 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS

I am sure I am not doing parallel runs on any other processor. It is
written in the GROMACS error analysis that' If you didn't think you were
running a parallel calculation, be aware that from 4.5, GROMACS uses
parallelism <http://www.gromacs.org/Documentation/Terminology/Threading> by
default. To prevent this, you can either give mdrun
<http://www.gromacs.org/Documentation/Gromacs_Utilities/mdrun> the "-nt 1"
command line option, or build GROMACS so that it will not use threads.
Otherwise, you might be using an MPI-enabled GROMACS and not be aware of
the fact.'

Therefore, according to the suggestion I have used the option -nt 1 in the
md run command line. The problem is the simulation is getting slower than
most of the other calculations I 've performed with the same system. Can
anyone tell me why is it so? I 've never done parallel computation to
accelerate the simulations. Also, with the option -nt 1 do I ensure correct
sampling of the system? I hope I'm not asking for much..

Thanks for your time in advance.

Soumadwip Ghosh
Senior Research Fellow,
IITB, Mumbai

More information about the gromacs.org_gmx-users mailing list