[gmx-users] One question about Domain decomposition

Berk Hess gmx3 at hotmail.com
Mon Feb 16 16:01:22 CET 2009


Your question is too vague for me to answer.
What do you mean with "all the molecules"?
And what do you mean with information?

Every node knows the topology of the whole system.
But each node only knows the coordinates and velocities of its local atoms
plus the coordinates of some atoms of neighboring nodes.


> Date: Mon, 16 Feb 2009 22:45:43 +0800
> From: xuji at home.ipe.ac.cn
> To: gmx-users at gromacs.org
> Subject: [gmx-users] One question about Domain decomposition
> Hi all Gromacs users:
> These days I read the codes about domain decomposition of Gromcas-4.0. 
> It seems that every node which is used to deal with one real space 
> domain has all of the molecules' information as in the particle decomposition. 
> Is my comprehension right? And if it's wrong how is the molecules' 
> information stored in domain decomposition of Gromacs-4.0 ?
> Appreciate any help in advance!
> Best 
> 	wishes!
>         xuji
>         xuji at home.ipe.ac.cn
>           2009-02-16

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