[gmx-developers] bonded interaction -- single molecule in parallel gmx?

Fan Hao f.Hao at chem.rug.nl
Tue Jul 29 12:11:11 CEST 2003

Hi, All:
        I am trying to parallelize my implicit solvent model in gmx
but I met a problem from bonded interaction. I use LINCS for the
constraint in my sd simulation The system is only a protein molecule so
when I did "grompp -np 2 ..., gmx try to split the molecule between the
shake border. I got the following error message from function

splitting topology...
Walking down the molecule graph to make shake-blocks
There are 255 charge group borders and 1 shake borders
There are 255 total borders
Division over nodes in atoms:
   282   280
Fatal error: Shake block crossing node boundaries
constraint between atoms (280,284)
I wonder whether there is a way to let the bonded interaction
be calculated by the home node or I have to build a seperated
mpi structure in my implicit solvent model and keep the normal
sd part to be single-processor simulated. Any help will be sincerely

Best regards

Yours sincerely

Hao Fan :-)

Drs. Hao Fan                            email F.Hao at chem.rug.nl
Lab. of Biophysical Chemistry
University of Groningen
Nijenborgh 4                            9747 AG GRONINGEN
The Netherlands

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