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
Received on Wed Oct 17 2001 - 07:32:02 PDT
