[gmx-users] Multiprocessor problems

[Sampo Karkola]

Dear users,

I'm running md simulations for a protein in water with ions and ran into
some problems when I started using a multiprocessor computer. I have several
runs with and without substrate or water molecules in the active site. I was
able to energy minimise and run a restricted dynamics simulation on them
with no problems with the multiprocessor machine but when I tried the free
dynamics I encountered several problems.

One mdrun doesn't start because it complains about an iron-coordinated
sulfur having more than 10 bonds. I checked the structure file but
everything seems to be ok. I tried the mdrun on a single processor machine
and it worked fine. The only difference between the mdruns was the number of
nodes defined during grompp. I noticed that someone else had a similar
problem earlier in the list but as far as I searched, there were no answers
to him. So, if someone knows how to fix this, I'd be grateful.

Secondly, again in multiprocessor machine, one mdrun doesn't start and I get
an error message saying "Format exec error. Binary file not executable".
Again, this works fine in a single processor mode and the only difference is
the number of nodes defined during grompp.

All help is highly appreciated,

Sampo Karkola



*********************************************
Sampo Karkola, M.Sc.
Scientific researcher, Teaching assistant
Laboratory of Organic Chemistry
Department of Chemistry
PO Box 55
FIN-00014 University of Helsinki
Finland

e-mail: Sampo.Karkola at helsinki.fi
http://www.physics.helsinki.fi/~karkola
tel:    +358 9 19150369 Work
        +358 50 5871175 Mobile
fax:    +358 9 19150366