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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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