[gmx-users] mpi version

[David van der Spoel]

On Wed, 2004-06-09 at 14:35, Prasad Gajula wrote:
> Dear Gromacs Users,
> 
> when I make simulations for my molecule using the mdp opton
> constraints=none or hbonds, it is running well on 2 nodes( i.e 4
> processors)
> but, when I use the option constraints=all-bonds grompp giving an error
> message like this.......
> Checking consistency between energy and charge groups...
> splitting topology...
> Walking down the molecule graph to make shake-blocks
> There are 3754 charge group borders and 8 shake borders
> There are 13 total borders
> Division over nodes in atoms:
>      0  6047  2335   449
> Fatal error: Shake block crossing node boundaries
> constraint between atoms (5685,8748)
> 
> 
> But, when I use only one processor it is working well for constrints=
> all-bonds too.
> Could any one suggest me what should I do now to use 4 processors to work
> for my md simulations with mdp option constraints=all-bonds!

sorry, it's not implemented.

> PS: I am freezing the Backbone during my run..hope it is irrelevant.
> Thank you very much in advance!
> Best regards
> Gajula
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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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