Re: AMBER: using sander without SHAKE

From: David A. Case <case.scripps.edu>
Date: Wed, 24 Dec 2003 10:06:40 -0800

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 

-- 
==================================================================
David A. Case                     |  e-mail:      case.scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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10550 N. Torrey Pines Rd.         |  home page:                   
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Received on Wed Jan 14 2004 - 15:53:12 PST
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