Re: AMBER: using sander without SHAKE

From: Bill Ross <>
Date: Wed, 24 Dec 2003 11:03:43 -0800 (PST)

> > 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.

Moreover the TIP3 potential (derived for water-water interactions,
not water-solute) involves a large vdw centered on the water oxygen
and including the H's. Hence the distance between water O's and solute
atoms will be unrealistic. See

  Ion-Induced Stabilization of the G-DNA Quadruplex: Free
  Energy Perturbation Studies. W.S. Ross and C.C. Hardin
  Journal of the American Chemical Society 116, 6070 (1994)

for a description of how it was necessary to develop separate ion
parameters for ions surrounded by Amber ff atoms vs. ions in TIP3.

Finally, if allowing stretchable bonds involving hydrogens, remember
to run with a sufficiently short timestep to capture the bond stretching

Bill Ross

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Received on Wed Jan 14 2004 - 15:53:12 PST
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