[gmx-users] RE: RE: RE:RE: One question about Domain decomposition

Berk Hess gmx3 at hotmail.com
Tue Feb 17 14:03:36 CET 2009


Sorry, I don't have time to help you with that.
This is a mailing list for helping people with the use of Gromacs,
not for helping people develop there own code.


> Date: Tue, 17 Feb 2009 21:02:32 +0800
> From: xuji at home.ipe.ac.cn
> To: gmx-users at gromacs.org
> Subject: [gmx-users] RE: RE: RE:RE: One question about Domain decomposition
> Hi, Berk
> Thank you for your explain!
> I have a little parallel program about simulating long chain molecules. 
> Because of the difficulties in parallel, the atoms of the chain molecules
> are stored in the space grid. That is to say first I use domain decomposition
> to split the whole simulation space into several small domains, 
> and then in each domain I use the grids which are used in neighbor 
> searching to store the atoms. It's convenient to do neighbor searching this way, 
> but when I come to the bonds, angles and dihedrals forces it is hard to determine 
> every atom's connected bonds, angles and dihedrals atoms. Especially it's hard to 
> locate the memory position where the atom is stored according to its index.
> So I come to Gromacs-4.0 for the high efficiency of it. So actually the element
> of my program is atom but not charge group. So can you tell me a little more 
> detail about the way you store the atoms of the chain molecule in Gromacs-4.0 
> in domain decomposition? And how the bonds, angles and dihedrals are reconstructed
> in each local domain?
> Best
> 	wishes!
> Xuji
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