[gmx-users] Ions and charge groups

[Guido Polles]

Hi everybody,

Sorry about this, but I'm pretty new to gromacs and I couldn't find
any clue about my problem in the archives or in the manual.
I'm using gromacs 4.5.1, and my system is a rather big system (about
12x12x12) that includes a proteon, an atp molecule, water and some
ions.
I am using ffamber99sb force field. Now, I post the log for my mdrun.

  Initializing Domain Decomposition on 2 nodes
  Dynamic load balancing: auto
  Will sort the charge groups at every domain (re)decomposition
  Initial maximum inter charge-group distances:
     two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685
     multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686
  Minimum cell size due to bonded interactions: 16.294 nm
  Using 0 separate PME nodes
  Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
  Optimizing the DD grid for 2 cells with a minimum initial size of 20.368 nm
  The maximum allowed number of cells is: X 0 Y 0 Z 0

-------------------------------------------------------
Program mdrun, VERSION 4.5.1
Source code file: domdec.c, line: 6428

Fatal error:
There is no domain decomposition for 2 nodes that is compatible with
the given box and a minimum cell size of 20.368 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

Of course the main point here is this

  Initial maximum inter charge-group distances:
      two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685
      multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686

but they're CL ions! Why should they have any bonded interaction or
angle interaction??
Actually, I made some tests, and:

1- if I solvate the protein+atp+ions  (I want the ions to be in
specific positions) system I get that 14nm bond error when I run
mdrun, but grompp let it go.
2- in this situation, if I move in the gro file the coords for the
ions after the water, same happens but now grompp throws a warning
about charge group distance.
3- if I solvate then use genion to include the ions at least the
simulation starts. Then I get this error "A charge group moved too far
between two domain decomposition steps", but that is probably related
to my system

I really don't get what's going on here.
Thank you in advance for any feedback.

Guido