AMBER Archive (2001)

Subject: (no subject)

From: Xiaolin Chuang (xiaolin_chuang_at_hotmail.com)
Date: Thu Aug 23 2001 - 11:00:49 CDT

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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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