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

[David van der Spoel]

On Tue, 2003-07-29 at 12:11, Fan Hao wrote:
> 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
> split_force2():
> 
> 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
> appreciated!!
how about using only constraints for the H atoms?

there is no other simple solution.

> 
> 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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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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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