AMBER Archive (2001)

Subject: distribution of Na+ around DNA

From: Xiaolin Chuang (xiaolin_chuang_at_hotmail.com)
Date: Wed Oct 17 2001 - 07:04:54 CDT

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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
much.

Any suggestion is appreciated.

Thank you very much in advance.

Xiaolin

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