[gmx-users] shake-block problem

Jianhui Tian jianhuitian at gmail.com
Wed Oct 4 21:32:40 CEST 2006

Hi GMX-Users,

Does anyone have any idea about the problem? Thanks a lot in advance.

I got an error message when using gromacs on 2 processors on the same
The error message is like this:
splitting topology...
Walking down the molecule graph to make shake-blocks
There are 24390 charge group borders and 26054 shake borders
There are 24390 total borders
Division over nodes in atoms:
  21234   21234
Program grompp_d, VERSION 3.3
Source code file: splitter.c, line: 121

Fatal error:
Shake block crossing node boundaries
constraint between atoms (21226,21234)
I used h-bonds constraints.  I tried not
to without constraints and the system can be ran on 2 processors well, but
the time-step is small then.
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