[gmx-developers] d.lzm in the benchmark files?

[David van der Spoel]

On Wed, 2004-01-21 at 03:05, MailList wrote:
> Hi,
> 
> I trid to run gromacs with the data in d.lzm of the benchmark 3.0. But there
> are error messages when I run:
> grompp -c conf.gro cutoff.mdp topol.top -shuffle -sort -v -np 16
> This happened too for pme.mdp on 16 processors. But both them are ok on 1,
> 2, 4 and 8 processors.
this bug has been fixed in the 3.2.0beta release.

> 
> Any sugesstions? Thank you so much.
> 
> ======================================================================
> PS: the end of the error messages are:
> 
> splitting topology...
> Walking down the molecule graph to make shake-blocks
> There are 7882 charge group borders and 7846 shake borders
> There are 7429 total borders
> Division over nodes in atoms:
>   1453  1451  1449  1450  1450  1450  1450  1450  1450  1450  1450  1452
> 1452  1449  1452  1449
> Fatal error: Shake block crossing node boundaries
> constraint between atoms (1446,1453)
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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