AMBER Archive (2003)

Subject: Re: AMBER: Question about quasih analysis

From: David A. Case (case_at_scripps.edu)
Date: Mon Jul 28 2003 - 16:40:48 CDT

On Mon, Jul 28, 2003, Lishan Yao wrote:

> Thanks for the help. Now, it works. I get 3N-6 frequencies. I check the
> trajectory file, one CH2OH group and one NH2 spin. Probably that is the
> reson why I get some low frequencies. My question is : In nature, does
> it really spin, or just an artificial phenomenon of MD? My friend, a
> quantum chemistry guy, doesn't believe it should spin.

If you run a nanosecond of simulation, I would expect CH2OH groups to move
around quite a bit, creating apparent low-frequency quasih modes. Same is
probably true for NH2 groups, depending on what they are attached to. It all
depends on the effective barrier height and the temperature of the simulation.

..hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
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