distribution of Na+ around DNA

From: Xiaolin Chuang <xiaolin_chuang_at_hotmail.com>
Date: Wed 17 Oct 2001 12:04:54 +0000

Dear Experts,

I have run MD of poly AT 40 bases with explicit WAT and 38 Na+, input file
was attached. When I had a look trajectory file of 1500-2500 ps, I found
that Na+ ions are far from phosphate group. Is it normal result of MD? or
anything wrong in my input file? I attached picture of one snapshot
"mdpic.jpg" showing positions of Na+ ions. Other snapshots are almost the
same as mdpic.jpg, in other word, position fluctuation of Na+ ions is not to

Any suggestion is appreciated.

Thank you very much in advance.


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Attachment Converted: "c:\eudora\attach\runprodt.in"

Attachment Converted: "c:\eudora\attach\mdpic.jpg"
Received on Wed Oct 17 2001 - 05:04:54 PDT
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