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Hi,<br><br>Sorry, I don't have time to help you with that.<br>This is a mailing list for helping people with the use of Gromacs,<br>not for helping people develop there own code.<br><br>Berk<br><br>> Date: Tue, 17 Feb 2009 21:02:32 +0800<br>> From: xuji@home.ipe.ac.cn<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] RE: RE: RE:RE: One question about Domain decomposition<br>> <br>> <br>> <br>> Hi, Berk<br>> <br>> Thank you for your explain!<br>> I have a little parallel program about simulating long chain molecules. <br>> Because of the difficulties in parallel, the atoms of the chain molecules<br>> are stored in the space grid. That is to say first I use domain decomposition<br>> to split the whole simulation space into several small domains, <br>> and then in each domain I use the grids which are used in neighbor <br>> searching to store the atoms. It's convenient to do neighbor searching this way, <br>> but when I come to the bonds, angles and dihedrals forces it is hard to determine <br>> every atom's connected bonds, angles and dihedrals atoms. Especially it's hard to <br>> locate the memory position where the atom is stored according to its index.<br>> So I come to Gromacs-4.0 for the high efficiency of it. So actually the element<br>> of my program is atom but not charge group. So can you tell me a little more <br>> detail about the way you store the atoms of the chain molecule in Gromacs-4.0 <br>> in domain decomposition? And how the bonds, angles and dihedrals are reconstructed<br>> in each local domain?<br>> <br>> Best<br>> wishes!<br>> <br>> <br>> Xuji<br>> <br>> <br>> <br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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