AMBER Archive (2005)

Subject: Re: AMBER: Is the MD simulation normal

From: Shulin Zhuang (shulin.zhuang_at_gmail.com)
Date: Wed Jun 29 2005 - 05:11:53 CDT

Dear Prof. Duan and Prof. Ross,

Another important figure is attached.

I samples several snapshots from the NPT trajectory and superimpose
them. The ligand slide much away from the initial position.
Superimposition of the complex reveals that the RMSD of the protein is
relatively small, 0.8 or so. Indeed , the backbone RMSD of the
protein along the whole trajectory is under 1.0 angstrom.

I spent one month or so to this problem and still not work it out .

Best regards 

-- 
   Shulin Zhuang
Chemistry Department 
Zhejiang University PRC
shulin.zhuang_at_gmail.com
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