[gmx-users] mpi version
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jun 9 14:56:53 CEST 2004
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
> 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
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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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