[gmx-users] MD vs. free energy simulations

Jernej Zidar jernej.zidar at gmail.com
Thu Aug 29 08:24:27 CEST 2013

  I ran some MD simulations (NPT ensemble) and a series of simulations
to determine the free energy of water solvation of a not to big

  I noticed that while I was able to run the MD simulations using all
the CPUs (or threads) in my workstation (12 CPUs or 24 threads,
respectively), whereas during free energy I can use 2 CPUs at most. If
I try to use more, the simulations would crash stating:
Program mdrun, VERSION 4.6.3
Source code file: /home/zidar/utils/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792

Fatal error:
There is no domain decomposition for 4 nodes that is compatible with
the given box and a minimum cell size of 4.52667 nm
Change the number of nodes or mdrun option -rdd or -dds
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

- - - -

  I can use more CPUs only if I switch from domain decomposition to
particle decomposition scheme. The size of the systems evaluated is
11.92513nm  x  5.44212nm  x 5.35234nm with ~30.000 atoms, so I assume
the size of the system is not an issue.

  Big question: Why is that so? Why can I use more CPUs for 'regular'
MD but only two for free energy simulations?

  I'd really like to use more CPUs as it would really speed-up the simulations.

Thanks in advance,
Jernej Zidar

More information about the gromacs.org_gmx-users mailing list