[gmx-users] shake-block problem

[David van der Spoel]

Jianhui Tian wrote:
> 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 
> computer.
> 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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please submit a bugzilla and upload your input files (top, gro, mdp).

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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