AMBER Archive (2001)

Subject: Re: distribution of Na+ around DNA

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Oct 17 2001 - 09:32:02 CDT

        I have run MD of poly AT 40 bases with explicit WAT and 38 Na+, ...
        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?

Yes. Ions will often form pairs with pairs of waters, in fact.
I don't know if this is physical behavior or not.

(mdin not inspected because not in clear text)

Bill Ross