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Dear Amber users,
I have run MD simulation of DNA (12 pairs) with explicit water and Na+ ions.
After 300 ps, by checking Temp, Etot, Density, and Pressure as well, I found
that the system is equilibrated. However, when I analyzed positions of Na+
ions, there were NOT near phosphate groups. IS IT NORMAL? I think that they
should be near phosphate groups.
Other question are that;
- What program can be used to analyze RDF (radius distribution function) of
water and Na+ ions? Can ptraj do this? if yes, what command?
- What program can be used to analyze structure of water?
Your suggestions are appriciated.
Thanks in advance.
Xiaolin
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Received on Thu Aug 23 2001 - 09:00:49 PDT
