[gmx-users] problem with Shake block crossing node boundaries

[Siavoush Dastmalchi]

Hi,

I don't know why I get the following error message when I use more than one node when I run grompp (e.g., grompp -np 32 .....). From previous emails, I gathered that I need to reduce the number of nodes. But for me it just works when I use a single node.

Any suggestions?  Cheers, Siavoush 

Here is the error:

Walking down the molecule graph to make shake-blocks
There are 556 charge group borders and 1 shake borders
There are 556 total borders
Division over nodes in atoms:
      41      41      42      40      42      42      44      41      42      41      42      42      42      41      42      40      43      42      41      41      41      42      40      41      42      40      41      37      42      43      41      42
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: splitter.c, line: 121

Fatal error:
Shake block crossing node boundaries
constraint between atoms (1270,1283)
-------------------------------------------------------


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