(no subject)

From: Xiaolin Chuang <xiaolin_chuang_at_hotmail.com>
Date: Thu 23 Aug 2001 16:00:49 +0000

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.


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Received on Thu Aug 23 2001 - 09:00:49 PDT
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