AMBER Archive (2003)

Subject: Re: AMBER: using sander without SHAKE

From: David A. Case (case_at_scripps.edu)
Date: Wed Dec 24 2003 - 12:06:40 CST

On Thu, Dec 25, 2003, Wayne Dawson wrote:
>
>
> But how can we really be so sure that __all__ the causes of solvation
> on electrostatic proteins can be fully accounted for by a rigid water
> model?

Of course, OH bond vibrations may play an effect. But to study this, you need
to use a water model that was designed to be flexible. Just removing the
rigidity constraints from TIP3P will generally not be sufficient. You might
also want to consider zero-point vibrational effects, which are not accounted
for in classical simulations of flexible waters.

..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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