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

MailList alantu9000 at hotmail.com
Wed Jan 21 03:05:18 CET 2004


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.

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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